The Stargate Program (SGC) is revived when Apophis, an alien of the same race as Ra, comes to Earth through the gate seeking hosts. After the attack, Colonel Jack O'Neill and Samantha Carter are sent to Abydos to locate, and bring back, Daniel Jackson. O'Neill and Daniel befriend Apophis's first prime Teal'c, a Jaffa (one who is an incubator to a larval Goa'uld), and Teal'c joins their side. He helps SG-1 return to Earth, though they cannot save Daniel's wife Sha're and his friend Skaara, who have been taken as hosts.

After being infested by a Goa'uld parasite in the previous episode, Major Charles Kawalsky shows signs of possession. The symbiote is removed, but Kawalsky remains possessed and is killed by Teal'c.

SG-1 visits a planet inhabited by the Shavadai, a nomadic tribe descended from the Mongols. They regard women as property, and restrict their rights in the belief that to do otherwise would bring demons (the Goa'uld) down upon them. Carter ends up being 'sold', but when Carter beats a chieftain in hand-to-hand combat, the team changes the tribe's opinions about the rights of women. Guest starring Soon-Tek Oh and Cary-Hiroyuki Tagawa.

SG-1 travels to P3X-797, a planet divided into 'Light' and 'Dark' sides. While the inhabitants of the light side have a Bronze Age culture bearing similarities to the Minoan civilization, the dark side is infected with a plague that turns people into savages, and the SGC is locked down when SG-1 brings it home. Dr. Janet Fraiser manages to find a cure for both peoples.

As SG-9 is on P3X-513 and long overdue, SG-1 is sent after them to find out what has happened to them. They soon discover that the commander of SG-9 has gone completely insane and set himself up as a god on the planet.

A strange crystal strikes down O'Neill, replacing him with a double that returns with the team to Earth to find the cause of O'Neill's private grief – his son's death. But the double is dangerously unstable. Can O'Neill return home to save everyone and prevent chaos?

When a planned ambush goes disastrously awry, resulting in fatalities among the SG-1 team, the peace-loving Nox restore them to life. But while these gentle people can bring back the dead, can they resist the deadly technology of the blood-thirsty Goa'uld?

On the mysterious planet Argos, the beautiful Kynthia (Bobbie Phillips) seduces Colonel O'Neill, which means he is condemned to an Argosian lifespan of only a hundred days. As he turns grey and old, will his team succeed in their frantic search for a cure?

SG-1 visits the planet Cimmeria (P3X-974), a planet inhabited by Viking descendants, in search of allies against the Goa'uld. Upon arrival, O'Neill and Teal'c are trapped in a labyrinth, where the only exit is through Thor's Hammer, a device to destroy Goa'uld, but preserve the host. Goa'uld weapons are rendered inoperative but not earth guns.

SG-1 goes to Heliopolis (PB2-908) and recovers Dr. Ernest Littlefield, who went through the Stargate in 1945 (using a standard diving dress as a spacesuit) and never returned. Daniel nearly stays behind to study a 'book' detailing the meaning of human existence, left behind by the Four Great Races.

Teal'c's son Rya'c is to be implanted with his first Goa'uld larva on Chulak, so SG-1 goes to prevent it. However, Rya'c falls ill and can only be saved by a symbiote; Teal'c donates his own, and receives a stolen one for himself. The team also meet Teal'c's first teacher Bra'tac, formerly the greatest of all Jaffa warriors and now still a spry 133 years old, who had taught Teal'c that the Goa'uld were false gods.

On P3X-866, SG-1 is given a false memory of Daniel's death by his alien abductor Nem. Nem is a member of an amphibious species named Oannes (Ohne), and wants to know from Daniel what happened to his mate Omoroca in ancient Babylon. Ultimately, Daniel remembers the obscure fact from his studies of ancient myths, and is allowed to go home.

The Goa'uld Hathor (one of the mothers of all Goa'uld) brainwashes the men of the SGC with pheromones, and nearly makes O'Neill host to a larval Goa'uld conceived with Daniel. She flees after the unaffected women of Stargate Command retake the facility.

On the planet Hanka (P8X-987), SG-1 rescues Cassandra, a small girl who turns out to have had an inoperable Naqahdah bomb put in her by Nirrti to destroy the SGC. Ultimately the girl is given to the care of Dr. Janet Fraiser, the SGC doctor, after they discover that the bomb will dissolve if she is kept away from the Stargate.

The Byrsa, human inhabitants of the planet Cartago (P3X-1279) that was once enslaved, condemn Teal'c for the atrocities he once committed under Apophis. He is sentenced to death, but when the Goa'uld attack, Teal'c saves his accuser's life and proves he is a changed man.

SG-1 rescues a group of highly advanced Tollan from their homeworld, P3X-7763. The military and the NID take an interest in their technology, and attempt to imprison them for research purposes before Daniel helps them take refuge with the Nox.

Carter and O'Neill are stranded on an icy planet when the Stargate malfunctions on their return journey to Earth. However, it turns out that they have merely been redirected to a second Stargate in Antarctica.

11,000 years ago, the inhabitants of the planet On Altair (P3X-989) were forced underground by deadly radiation, and eventually transferred their minds into exact android duplicates to survive. By the time SG-1 visits their planet, there is only one remaining individual, Harlan, who creates android replicas of the Earth team to aid him. When this is discovered, the androids must accept that they will stay off-world, and the real SG-1 returns home.

On P3R-233, Daniel finds a strange alien mirror and is accidentally transported into an alternate universe where he finds things are completely different from his own reality. Before he returns, he learns that Apophis will attack Earth in ships from a certain Stargate address.

Senator Robert Kinsey shuts down the Stargate program (as the gate represents a global risk and costs too much money to operate), despite Daniel's warnings that Apophis will attack Earth, and that the Stargate may be Earth's only defense.

SG-1 uses the Stargate to go to an address discovered by Daniel Jackson. This turns out to be Apophis's ship, where they find that Skaara has been made host to Apophis's son Klorel. The ship reaches Earth, and the fate of the world hangs in the balance.

Teal'c's former mentor Bra'tac joins their fight and together they embark on a mission of planting bombs to destroy Apophis' ship and halt the attack on Earth. Eventually they destroy the two ships and escape in Death Gliders.

When the planet Nassya (P3X-382) falls under attack by the Goa'uld, Carter is possessed by a Goa'uld. When the Goa'uld is discovered, she claims to be Jolinar, a member of the Tok'ra, a legendary faction of rebel-Goa'uld opposed to the System Lords. When Jolinar is assassinated, she saves the life of Samantha Carter.

After being sentenced to life imprisonment on the planet Hadante, SG-1 escapes with the help of a female inmate named Linea, who has great herbal knowledge. After they set her free, they discover she is known as the Destroyer of Worlds for once having deliberately created a vaccine that caused contagious sickness killing half the population of a planet.

SG-1 discover a world where all the people are enclosed in a virtual reality, believing that their planet is dead. SG-1 become trapped in the virtual reality, but inform the residents that their planet is beautiful again, and they all go free.

Offworld, Daniel stops a young woman from killing herself. She turns out to be the daughter of Pyrus the Godslayer, the ruler of the planet who had overthrown the Goa'uld overlord but to keep the other Goa'ulds from finding out, he keeps the people virtually enslaved and sends back naqahdah. She falls in love with him and uses the narcotic properties of the Sarcophagus to keep him with her, but once home he is rehabilitated and eventually let back into SG-1. He visits the woman, whose father had died, and she promises to improve the lot of her people.

SG-1 returns to Cimmeria (Thor's Hammer) to help defend the planet when the Goa'uld invade. They contact Thor who shows himself as an Asgard. He is annoyed with SG-1's interference but comes via ship and eliminates the invasion nevertheless.

SG-1 brings back a mysterious sphere from P5C-353. The sphere suddenly sprouts rods that impales O'Neill's shoulder, pinning him to the wall. After attempts to remove it, SG-1 discover it contains microscopic aliens that feed on energy who are the last of an alien race. They eventually agree to be relocated to P4G-881, a planet that is a more suitable home than Earth.

Bra'tac brings word that Apophis has kidnapped Teal'c's son Rya'c. Returning to Chulak with SG-1, Teal'c finds that his son is brainwashed and loyal to Apophis. Apophis had implanted some deadly pathogen on Rya'c which would have destroyed all life on earth if activated. They resort at last to zat-blasting Rya'c to overcome the brainwashing chemical.

Having to fulfill a promise to Sha're's father Kasuf, Daniel and Teal'c return to Abydos. Upon their arrival, Daniel learns that his wife, after having been captured by the Goa'uld, is now pregnant by Apophis. On earth, the Stargate Program is under risk of being exposed by a reporter.

Teal'c is stung by a strange insect while exploring BP6-3Q1. Upon returning to earth, the virus begins changing Teal'c's DNA into its own. He escapes the SGC and develops a friendship with a young girl, Ally, and is ultimately cured.

SG-1 discovers a migratory people descended from the Native American Salish tribes on PXY-887. The Salish refuse to allow the SGC to mine their planet's large deposits of the valuable metal trinium, believing it would upset the spirits of the natural world. Under pressure from above, General Hammond orders mining to proceed without Salish permission, incurring the ire of their spirits, in fact advanced aliens who freed the Salish from the Goa'uld a millennium ago. The Salish Spirits attack the SGC, until SG-1 convinces them that burying their Stargate would be a better solution than destroying the base.

Jolinar (In the Line of Duty) has left a mental imprint on Carter, who dreams of the Stargate address of the hidden Tok'ra base at P34-353J. While SG-1 find and liaise with the Tok'ra, Carter's father Jacob is dying of cancer.

SG-1 offers an alliance with the Tok'ra, but it is turned down because Earth doesn't have enough to offer. Meanwhile, Selmak is a Tok'ra whose host is dying and the alliance deal is re-kindled when Jacob offers himself as a new host.

Inhabitants of the planet Madrona accuse SG-1 of stealing 'the Touchstone', an artifact that can control their planet's weather. The Madronans claim that men dressed in SGC uniforms took the device, and SG-1 suspect that maybe the thieves are using the second gate found in Antarctica.

SG-10 is stranded on planet P3W-451, which is close to a newly formed black hole. The SGC opens the gate to find out what happened, but they cannot shut it down afterwards. Soon they realize that since the planet is near to a black hole, its intense gravity is causing time dilation, so if they do not shut down the gate very soon, it will destroy the SGC, and in time, the entire planet.

On P3R-272, O'Neill is grabbed by an Ancient Repository of Knowledge, and has alien knowledge downloaded into his mind. Before Jack's mind is overrun, he discovers a gate address to the Asgard homeworld, who remove the information from his brain, saving his life.

Apophis's death glider crashes on PB5-926. Dying, he is brought to the SGC. The Tau'ri wish to interrogate him, however Martouf warns them that Sokar and many other Goa'uld want him.The Tau'ri fail to heed his warning and Sokar tries to attack Earth as he wants Apophis, but is stopped when they hand over the dead Apophis. However, Martouf informs them Sokar will use a sarcophagus to revive him and torture him indefinitely.

SG-1 meets an elderly man called Machello and learns that he has been hunted by the Goa'uld his entire life due to his inventions of technological devices meant to oppose them. Machello convinces Daniel to grasp a device made to switch bodies, and then escapes, leaving Daniel to die in the old body of Machello's.

After a UAV crashes into a large white plant on PJ2-445, SG-1 encounters inhabitants who appear to be dying en masse. SG-1 discover that the aliens depend on the large plants for survival because of an essential infrasound they emit, and rectify the situation.

A young boy warns SGC of a plot by invisible non-humanoid aliens (rogue Re'tu, who exist in large numbers on P63-2031) to destroy all humans. A minority of the Re'tu wage war on the Goa'uld by eliminating their potential hosts: humans. They operate in 5-man suicide units, which are capable of setting off an explosion equivalent to a small tactical nuke. SG-1 decide his warning is real, and call the Tok'ra for help, who provide TER's that locate the Re'tus already hiding on the base, and eliminate them.

When SG-1 steps through the gate to P2X-555, a solar flare sends SG-1 back in time. They meet a young General Hammond, then a lieutenant, who helps them due to a note (Help them, plus dates of what Carter figures out must be solar flares). They find the Stargate of 1969 and activate it during another solar flare, returning home.

O'Neill, Carter and Daniel awaken from stasis in what appears to be the SGC, almost 79 years in the future. They discover it is actually a Goa'uld hoax by Hathor. Meanwhile, Teal'c leaves the SGC to find SG-1.

The SGC sends a rescue mission to Hathor's base to retrieve SG-1, and O'Neill kills Hathor. Using Tok'ra tunnels already present on the planet, SG-1 escapes and returns home.

A Goa'uld named Seth has lived on Earth for thousands of years and now is the leader of a dangerous cult. SG-1 uses zats to overcome the cult members' brainwashing, and in the ensuing rescue, Seth is killed by Carter.

Captain Carter is promoted to the rank of Major. The Asgard warn the SGC that the Goa'uld are planning an attack on Earth. With the help of the Asgard, SG-1 negotiates with three Goa'uld System Lords, Cronus, Nirrti, and Yu, to bring Earth into the Protected Planets Treaty.

On PY3-948, SG-1 finds corpses of several humans who had clearly once had Goa'uld symbiotes. Upon returning, Jackson shows signs of schizophrenia. The cause is a Goa'uld-killer of Ma'chello's (having a strange effect on a non-Goa'uld), and the devices are neutralized.

SG-1 visits a planet named Orban where knowledge is harvested through its children (called Urrone). When a Urrone reaches a certain age, their nanites are harvested and they regress to an infantile state and remain that way as the Orbanians have no concept of traditional education.

Using the mirror from There But For the Grace of God, an alternate Carter and Charles Kawalsky come to the SGC from an Earth that has been invaded by the Goa'uld. SG-1 saves the alternate reality by contacting the Asgard there.

SG-1 is captured by a bounty hunter who uses them to help catch a Tok'ra. The Goa'uld has his race addicted to a drug that can be supplied only by them, but he repents at the last moment and asks Sam to help free his race from the drug.

SG-1 visits a planet ruled by a Goa'uld-infested Unas, who uses the persona of the Devil to keep the residents ruled by fear. They free the people of the 'devil' and instruct them to bury the Stargate.

SG-1 discovers a planet where Apophis was training human slaves to infiltrate the SGC. SG-1 shows them footage of Apophis dying, and they all renounce him as a false god.

After being found on P8X-873, Daniel's wife Sha're is killed by Teal'c to prevent the Goa'uld controlling her from killing Daniel. Jackson then starts seeing visions of a residual thought transferred to him by Sha're in the last moments – he must find her son Harcesis.

SG-1 travels to a world named Vyus (P2Q-463) where the people have lost their memories in an event called the Vorlix and are in search of their Elders. The Vorlix was following a visit from Linea (The Destroyer of Worlds, Prisoners), and they feel responsible for the problems on Vyus. Ke'ra, a young woman with vast knowledge about biochemistry, who assists them to research the world's past, connects strongly with Daniel.

Jacob/Selmak is captured by Sokar. Jolinar was the only person to escape from Sokar's home moon Ne'tu near the planet Delmak, and Carter has residual memories of the method. SG-1 is captured, and discovers that Apophis controls the moon.

SG-1 manages to escape from Ne'tu with Jacob and Selmak and make it back to Earth, using a Tok'ra bomb that blows up the moon and destroys Sokar's ship, killing Sokar with it. Apophis, however, escapes, and has risen again.

Stargate Command is under control by aliens originating from P3X-118. They use a frequency-based technology that allows them to mimic the appearance of other beings, i.e. humans. Carter must ask Colonel Maybourne to help her retake the base.

Skaara/Klorel crash lands on the Tollans' new homeworld Tollana and the Tollan invite SG-1 to represent Skaara in a trial to decide whether Skaara or Klorel has the right to use Skaara's body. Skaara wins. Lya of the Nox and SG-1 prevent a Goa'uld attack on Tollana.

The members of SG-1 are implanted with an AI named Urgo. They manage to rectify the problem by visiting Urgo's creator on P4X-884, who implants Urgo in himself instead to improve his personality.

A friendly planet named Edora (P5C-768) will be destroyed by meteorite bombardment soon. Stargate Command moves most of the population to another planet but O'Neill is trapped. SG-1 uses a particle beam to breach the iris that formed over the offworld gate, and retrieve O'Neill.

After stealing technology from the Tollan, O'Neill is forced to retire. He joins a rogue SG team dedicated to obtaining advanced technology by any means and then store them on . However, O'Neill was actually on a secret mission as a double agent to find and capture the rogues. He also comes across the Tiernod, a cave-dewelling race on PX3-595 under the protection of the Asgard, who gave them invisibility devices to hide from predators.

SG-1 visits a planet designated P2X-416 where the countries of Bedrosia and Optrica are in the middle of a war about the origin of life. The Bedrosians, who believe a Goa'uld created humans on their world, mistake SG-1 (minus Teal'c) for infiltrators and refuse to accept their account that the Stargate is a transportation device as the Optricans have always claimed. Teal'c frees his team with help from Nyan, one of a minority of Bedrosian scientists willing to approach the Optrican position with an open mind.

Daniel knows that the Harcesis is on a planet called Kheb; Bra'tac knows how to get there as it is the planet that the Jaffa believe to be the destination of their soul after death (P9C-292). They find a Zen monk who teaches Daniel about the ways of Ascension and an ascended being (Oma Desala) saves the child.

SG-1 finds a Mayan ziggurat in a lepton-rich environment on planet P7X-377; inside is a crystal skull that makes Daniel a ghost. Daniel's grandfather Nicholas Ballard found a similar skull in Belize and helps out. When they return to the planet, giant aliens who have vaguely humanoid but insubstantial forms, appear and return Daniel to normal.

Thor's starship has been infected by Replicators. In order to keep it from landing on earth, SG-1 disables the deceleration engines so the ship burns up in the atmosphere and crashes in the Pacific. While they attempt escape to P3X-234, one replicator remains.

The Replicator on Earth has reproduced and taken over a submarine; O'Neill and Teal'c neutralise the threat. Carter goes with Thor to defend the Asgard homeworld from the Replicators. They use the Asgard's newest ship (named the O'Neill) to lure the Replicators into hyperspace, where the ship is blown up.

Humans on the planet Euronda contact Stargate Command for help; they are fighting a losing war against an enemy they call the Breeders and have run out of food and fuel supplies. SG-1 travels to Euronda and make an alliance to trade heavy water for advanced technology to combat the Goa'uld. But SG-1 discovers their new allies are guilty of mass genocide against the Breeders. SG-1 then sabotages the base and it is destroyed.

The Tok'ra Anise gives Atanik arm devices to O'Neill, Carter, and Daniel that greatly increase their strength and speed. But the devices rely on a virus that is eventually neutralized by the human immune system, causing the members of SG-1 to lose the strength they gained. However, they don't realize this until they are on a mission on PX9-757, a planet where Apophis builds a new prototype mothership.

The SGC is visited by Shan'auc, a female Jaffa who has discovered how to communicate with her larval Goa'uld symbiote and claims that she has information that could destroy the Goa'uld.

The Goa'uld can impose subconscious programming on humans. The Tok'ra have a test to detect the programming (by detecting lies) and when it is applied to the staff of Stargate Command, Carter and O'Neill are found to be affected. They were supposed to have been affected in Upgrades however it is discovered that Carter and O'Neill are subconsciously failing the test because of their feelings for each other. Feelings that they try and lie to avoid before realizing their mistake.

After an encounter with an Ancient time device on P4X-639, O'Neill and Teal'c get trapped in a time loop that only they know about.

The Russians have been using the second Stargate in secret, but after dialing a world that is completely under water, they lose contact with their Stargate facility and approach Stargate Command for help. The reason is discovered to be microscopic beings that live in, and control, water. They broke free and attempt to return home through the Stargate by controlling human bodies and emitting enough energy to keep a Stargate open indefinitely.

While helping with the excavation of fossilized Goa'uld on P3X-888, the homeworld of the Goa'uld and the Unas, Daniel Jackson is captured by the Unas Chaka. The rest of SG-1 tries to find him.

Earth resettles a group of Enkaran refugees, a race of humans who have become specifically adapted to their homeworld and thus require exact environmental conditions, to another planet, but an alien spaceship is transforming the new planet into a hostile environment.

The members of SG-1 have had their memories altered and been put to work in an underground industrial complex. They must recover their memories in order to escape.

An odd man called Martin Lloyd has inexplicable knowledge of the Stargate and claims that he is from outer space. He remembers his home address. He turns out to belong to a small group of men who deserted their homeworld after losing a war against the Goa'uld. After failing to find anything but more hardship, they chose to desert the rest of their race and hide out on Earth.

Teal'c and O'Neill test-fly the first experimental aircraft based on combined Earth and Goa'uld technologies, but soon a hidden trap in the aircraft takes control of the X-301 and propels it to the open space. Sam and Daniel enlist Jacob/Selmak's help to rescue them before the life support of X-301 is depleted.

Daniel's old professor has died. Daniel goes to the funeral and discovers a controversy surrounding the professor's death. SG-1 discovers that a Goa'uld, Osiris, has escaped from an ancient canopic jar the professor's team was studying.

The Tok'ra and Stargate Command want to sabotage a meeting of Heru'ur and Apophis, who want to form an alliance on neutral ground on the homeworld of the extinct Tobin race, descendants of the Phoenicians. The planet is surrounded by a minefield. SG-1 discovers Heru'ur has captured Teal'c and intends to use him as a peace offering. Jacob/Selmak plans to meet Teal'c and Rak'nor, a supposed friend of Teal'c's on the inside, on the third moon of the planet Tichenor.

Hammond abruptly resigns as head of the SGC, and is replaced by General Bauer. O'Neill suspects there is more to it than Hammond will admit and refuses to let the matter rest. General Bauer sends an SG team to the Goa'uld planet P3S-452 to obtain naqahdah.

In an alternate timeline, Earth has defeated the Goa'uld with the help of the Aschen, a bland and humorless advanced people from a world designated P4C-970. Earth discovers too late that the Aschen plan to depopulate the planet by secretly sterilizing much of the population through life-extending drugs. Thus, the former members of SG-1 sacrifice their lives to send a warning back in time to themselves not to contact the Aschen homeworld P4C-970. The season 5 episode 2001 resumes this story.

The Harcesis has come to visit the SGC and puts Jackson in a coma-like state. Jackson experiences what it means to have all the knowledge of the Goa'uld.

SG-1 discovers a world abandoned by the Goa'uld where there is a room with a beautiful, mesmerizing light display. But the light may have an insidious effect.

Carter meets a brilliant USAF cadet while lecturing at the Air Force Academy, but the cadet has a problem with authority. Carter decides to show her there are possibilities she isn't aware of. On an off-world mission on M4C-862, a moon 42,000 light-years from Earth, energy-based creatures take a dislike to the Tau'ri and Carter and the cadet must work on a solution to get everyone home. This episode includes a cameo by General Michael E. Ryan, then Chief of Staff of the United States Air Force. There is a Star Trek reference: the cadet refers to zats as those phaser things.

Stargate Command sends a probe through the Stargate to P9C-372, a world inhabited by electronic lifeforms. The base computer system is compromised by what is apparently a very advanced computer virus, which eventually displaces Samantha Carter's mind from her body.

After Cronus's army captures the android counterparts of SG-1 (Tin Man) on the planet Juna (P3X-729), the members of the real SG-1 must work with their robot duplicates to free the planet.

Apophis is on his way to Vorash, the planet the Tok'ra are using as a base. Carter and Jacob/Selmak attempt to wipe out Apophis' fleet by sending a Stargate linked to a black hole into the local sun.

After Apophis has brainwashed Teal'c, SG-1 and Jacob prepare to fight against their foe on board Cronus's ship. A mysterious ship then appears and attacks Apophis' ship, disabling it, and causing them to flee, giving SG-1 the chance to get on board. But danger lurks in the form of an army of Replicator bugs and an auto-destruct programme.

Teal'c has been saved from dying on Apophis' ship but remains loyal to his old master. Bra'tac uses an old Jaffa ritual that will either bring Teal'c back or kill him.

After falling unconscious, Carter returns from Velona (P3X-636), a planet full of ruins, suffering from suspected exhaustion. But she begins seeing a mysterious young man named Orlin who can walk through solid objects. But everyone believes that she's seeing things.

O'Neill remains on a planet designated P7S-441 to protect Lieutenant Tyler, a fifth member of SG-1 whom only the other members of SG-1 can recall. Back on Earth, Hammond informs the team that Tyler doesn't even exist while Col. Simmons returns, seeking to shut the SGC down, citing the latest alien mind games as a possible safety risk.

SG-1 travel to K'Tau (P39-865) and discovers that the sun has been shifted to the infrared end of the spectrum. All life on the planet is doomed, and SG-1 are responsible. The planet's inhabitants are Norse people and worship the Asgard, and believe that the reddening sky is a sign from their Gods. In reality, the event is a solar reaction caused by SG-1's wormhole that spells death for the planet and its people.

Dr. Fraiser's adopted daughter, Cassandra, enters puberty and begins developing telekinetic abilities, but the strain of producing so much energy is causing multiple organ failure. Fraiser and SG-1 fear that they might not be able to stop the life-threatening changes caused by Goa'uld Nirrti's genetic experiments.

Chaka, the Unas whom Dr. Jackson befriended, has been kidnapped and taken to a planet where humans use Unases as slaves. On a rescue mission, Jackson is risking not only SG-1's safety but also an age-old system.

SG-1 gets trapped in an ancient ziggurat on P2X-338 along with a Russian team. Here they discover the remains of the original Russian team who had gone missing and there's also a Goa'uld on the loose, one who's willing to kill and inhabit anyone it wants with the sole intention of escaping.

The Tollan, in a highly unusual change of policy, agree to share advanced technology with Earth but Carter's friend, Narim, warns that this might spell great danger for Earth.

SG-1 visits an agricultural planet (P3A-194) inhabited by the Volians, who introduce them to their more technologically advanced allies, the Aschen, who propose an alliance with Earth. After Daniel Jackson and Teal'c discover the Aschen's world to be the gate address they forbade themselves from dialing (2010), Earth severs all contact with the Aschen.

Carter is kidnapped by a dying millionaire, forcing O'Neill to team up with Harry Maybourne in order to find her.

When Stargate Command learns of a television show whose premise closely resembles its operations, SG-1 investigates. They find that an alien named Martin Lloyd (Point of No Return) is giving the producers their ideas.

SG-1 is running training simulations for a group of new recruits. Things begin to get more serious when aliens invade.

SG-1's mission on P3X-116 runs into some difficulty when they come under fire from some Goa'uld with Tanith being the leader in question but Teal'c's return to Earth is interrupted when the destroyed mothership comes crashing into the Stargate, severing the wormhole and leaving Teal'c trapped in the Stargate. With a deadline of 48 hours bearing down on them before normal operations resume, SG-1 must work against the clock to find a way to save Teal'c before he is lost forever. As Daniel and Major Paul Davis attempt to make a deal with the Russians, O'Neill finds himself forming an unlikely partnership with rogue agent Harry Maybourne as General Hammond deals with Colonel Frank Simmons while Carter finds herself collaborating much to her own disgust and anger with Dr. Rodney McKay (David Hewlett), the world's foremost expert on the Stargate and who has already started believing that any chance of saving Teal'c is long gone.

There is a truce among the Goa'uld and the System Lords meet on a heavily guarded space station. The Tok'ra plan to kill them all, but require a human who can speak fluent Goa'uld and Daniel is the only qualified candidate. The Tok'ra create a version of the Reol chemical (The Fifth Man) for the undercover mission. Meanwhile, Anubis attacks an outpost of Kali on the planet Cerador, destroying two motherships. Lord Zipacna, under orders from Anubis, attacks Revanna, the site of the main Tok'ra base after Vorash.

A powerful System Lord shows himself for the first time in a thousand years and offers to destroy the Tau'ri and Tok'ra. Meanwhile, SG-1 and Lt. Elliot/Lantash are trying to escape the Tok'ra base.

An amateur astronomer discovers a rogue asteroid on a collision course with Earth. SG-1 and a couple of engineers repair the cargoship that crashed on Revanna and head for earth. Just before they reach the asteroid, there is a problem with one of the engines. They start heading for the asteroid, but manage to stop at the last moment. Teal'c and O'Neill place a naqahdah enhanced nuclear weapon. Carter discovers that the core of the asteroid is composed of naqahdah, so exploding the nuke would destroy Earth. They manage to use the ship's hyperspace engines to transfer the asteroid to the other side of earth.

The Jaffa rebellion has a new leader named K'tano, who seems almost too good to be true. SG-1 visits K'tano's Jaffa camp on the planet Cal Mah (meaning sanctuary) to negotiate an alliance. However, K'tano sends rebel Jaffa on a suicide mission to a stronghold under the control of Nirrti, and when K'tano sends Teal'c on a suicide mission against the Goa'uld system lord Yu, he finds that the new leader isn't what he seems.

The team finds an android that somehow managed to survive a Replicator attack. They learn she is the mother of all Replicators, but has the mentality of a young child. Danielle Nicolet guest stars as Reese.

The Latonans are a once-advanced race that abandoned technology to focus on mental development. Their homeworld Latona (P2A-018) is defended by a 500-year-old device called the Sentinel, which was inadvertently deactivated by rogue NID operatives seeking to reverse-engineer it. With Latona being invaded by the Goa'uld Svarog, SG-1 brings the NID agents with them to repair the Sentinel and save the Latonans from the Goa'uld.

Daniel incurs lethal radiation exposure when he prevents a potentially cataclysmic accident in a weapons laboratory on the planet Langara (P9Y-4C3). While the alien government responsible for the lab accuses him of attempting to sabotage their research, the Kelownan Jonas Quinn tries to negotiate with SG-1.

As Jack, Sam and Teal'c struggle to come to terms with losing Daniel, an Asgard scientist Heimdall is stranded on Adara II, a planet under attack by the Goa'uld. As the Asgard have no spare ships, they ask Stargate Command, particularly SG-1 to help, using their salvaged Goa'uld cargo ship.

As SG-1 and the SGC struggle to cope with Daniel's departure, they find themselves facing a new threat in the form of System Lord Anubis who has launched an attack against Earth by using an ancient weapon which will trigger a huge overload of energy directly into the Stargate and if the attack is successful, the entire planet will be destroyed. As the SGC scientists scramble to find a solution, Carter finds her abilities as both a scientist and military officer being put to the ultimate test with her woes later increasing when her rival, Dr. Rodney McKay (David Hewlett) later returns to the SGC from Russia, having been ordered to do so by the Pentagon while Jack still refuses to let a Russian soldier join SG-1 despite pressure from both Chekov and General Hammond while Teal'c goes offworld after learning that his wife is gravely ill and is left devastated when he learns that she has actually died. After learning that Earth is under attack, Teal'c, Bra'tac and Rya'c embark on a dangerous mission to find and destroy the weapon at any cost.

With the plan to contact the Asgard having failed, the SGC are left on their own and Carter attempts to find a solution while she continues to deal with McKay's unwelcomed presence. Meanwhile, Teal'c, Bra'tac and Rya'c prepare to launch an attack on the planet which has Anubis's weapon while Jonas later gives Carter an idea at saving the planet but it could result in Earth losing their Stargate and the Stargate Program being shut down for good.

SG-1 attempts to salvage a Goa'uld mothership that has been mysteriously abandoned in space near Earth. Unfortunately, the ship crashes in the ocean. SG-1 discovers that Thor's consciousness is still in the central computer.

The Antarctic team investigating the site where the second Stargate was found discovers a frozen Ancient. The team starts to suffer the effects of a deadly virus and while she helps to heal the infected, it becomes clear that it's taking a toll.

Bizarre behavior in a small American town proves to be the result of Goa'uld activity.

O'Neill has been captured by Ba'al but is being held in a fortress too well protected for Stargate Command to help. However, Jonas believes that Lord Yu might be persuaded to lend assistance.

The Kelownan government contacts the SGC, offering to exchange naqahdriah for advanced technology. Jonas's old professor asks him to help a secret resistance group and prevent a world war.

Dr. Felger worships SG-1, and when he has the chance to rescue them from a Goa'uld mothership, he doesn't hesitate.

The Jaffa rebellion, the Tok'ra and their base commander Malek, and Stargate Command are temporarily forced to share Earth's Alpha Site (a secret refuge) when the Tok'ra are attacked. Suspicion between the Tok'ra and the Jaffa turns hostile when a series of murders occurs.

SG-1 visit Pangar, a planet once ruled by Ra. The Pangarans offer a wonder drug called Tretonin in exchange for gate addresses, but fail to mention that the drug is produced by using the progeny of the former Tok'ra queen Egeria. The drug also destroys the user's immune system, causing a crisis when supplies ran low. SG-1 calls in help from the Tok'ra Malek and Kelmaa. After Egeria is freed by the Tok'ra Kelmaa, she tells the remorseful Pangarans how to free themselves from the tretonin.

A reporter has information about the Stargate Program and threatens to broadcast it on television. The SGC offers a deal to allow her access to the Prometheus on the condition that nothing is aired until the Stargate Program is made public.

The Asgard have called all the Replicators in the Asgard galaxy to one planet, Halla, but the time dilation device that was meant to trap them on the planet has failed to activate. The Asgard want SG-1 to use the Prometheus to find out why.

On a deserted planet designated P9X-391, SG-1 discovers a piece of Ancient technology. When it's moved to Earth for study, people begin to have inexplicable hallucinations.

Senator Kinsey is shot, and all the evidence seems to show that O'Neill was the assassin.

Maybourne offers to help the SGC find a cache of advanced alien weapons, but he is not telling them everything he knows.

The Russian team discovers a planet where Nirrti has been experimenting on the human population to create the perfect host.

The Americans and the Russians reveal the existence of the Stargate to the Chinese, French, and British governments. Senator Kinsey tries to use the meeting to hijack the program, but Hammond has a card up his sleeve.

SG-1 finds a wrecked spacecraft whose crew claims to have been fighting off aggressive aliens ever since they crashed. It later turns out that the crew are in fact prisoners of the Serrakin ship Ceberus. The Serrakin are an advanced race who once helped free the human Hebridans, descendents from the Celts, from the Goa'uld millennia ago. Since then, the two peoples have lived together in a largely harmonious society on the planet Hebridan.

Teal'c finds himself jumping between different realities of Earth and the planet Kresh'ta, where a meeting of 108 Jaffa rebel leaders are ambushed by the Goa'uld System Lords. Only Daniel seems to display any understanding of reality.

On the maiden flight of the finished Prometheus, the reactor overloads, and SG-1 must find the Stargate buried on the alien planet Tagrea in order to obtain spare parts from Earth. Tagrea was once ruled by the Goa'uld Heru-ur, and the memory of his occupation was so traumatic that the Tagreans buried their Stargate and wiped out all traces of their earlier history, so as to make a new start. Despite opposition from xenophobic elements of the Tagrean military, the progressive Chairman Ashwan assists SG-1 in locating the Stargate and eventually opens relations with Earth.

SG-1 finds a planet where the population worship Ba'al and work in the mines to provide his representative, Lord Mot, with a tribute of naqahdah. SG-1 intends to stop him, but things get complicated when Jonas starts seeing visions that could kill him.

Daniel contacts Jack O'Neill and tells him that Anubis has located the Eye of Ra, an enormously powerful weapon. SG-1 must get the Eye from Abydos, before Anubis. Anubis appears over the planet and threatens to destroy it.

Daniel is found living on Vis Uban (place of great power, P4T-3G6), a planet where the Ancients began building their greatest city when they were struck by a plague. Although Daniel has total amnesia, he helps SG-1 destroy Anubis' superweapon.

With knowledge of naquadria, Anubis attacks Kelowna and SG-1 must come up with a plan to save them.

O'Neill wakes up one morning to find himself 30 years younger, much to the annoyance of the Colonel. It is soon learned that the same process that caused him to become younger is also causing him to die.

Teal'c is shot by a Jaffa as they retreat through the gate and his self-confidence is greatly wounded. Meanwhile, Jackson remembers that Rya'c and Bra'tac are held prisoner on the planet Erebus where Jaffa prisoners of war must build Ha'tak ships. Teal'c must regain his confidence if they are to be saved.

Mahg Mar (P3X-289) has a toxic atmosphere but there is a forcefield dome protecting an idyllic village. That is, idyllic except for the fact that its inhabitants are disappearing one by one without noticing it themselves.

While exploring P2A-347, SG-1 encounters the crashed alien space ship Stromos containing a plethora of cryogenic pods. The team separates, and Daniel's mind becomes host to many different minds of the ship's crew. When SG-1 investigates the alien ship to find a way to cure Daniel, they discover that the minds of the passengers from the planet Talthus are being saved in the ship's computer.

SGC have found a planet with rich deposits of Naqahdah but the local population of Unas do not welcome the mining team.

Carter helps the Serrakin Warrick (season 6's Forsaken) to enter his spaceship in a dangerous race on his planet Hebridan (P4X-131). The prize is a lucrative contract.

Felger (The Other Guys) is about to be fired and desperate to persuade General Hammond to give him another chance. He invents a computer virus able to deactivate a Stargate, and targets one of Baal's principal naquadah mining sites on P5S-117 to test out the virus. However the virus spreads on its own and the entire network is shut down.

SG-1 meet a group of all female Jaffa from a planet named Hak'tyl (meaning liberation), who have set up their own rebel base. They were rebels against the Goa'uld Moloc who forced his Jaffa to sacrifice their female babies in fire; many of these female Jaffa were rescued as infants by their leader Ishta (Jolene Blalock).

Teal'c and Bra'tac are attacked by a black armoured warrior, impervious to all known weapons, who is found to be a human Goa'uld mutant created by Anubis. Daniel visits Honduras to find a hidden artifact which may hold the key to defeating them.

O'Neill goes to Honduras to rescue Jackson and in the meantime Carter, Jacob/Selmak and Teal'c must destroy the facility on the planet Tartarus where Anubis is creating the new warriors, using a Goa'uld queen to spawn new symbiotes.

Carter is on the Prometheus while the ship is on its way to Earth, and is attacked from a spaceship of a type they have never seen before. They try to escape by hiding in a nebula but all the crew except Carter disappear.

Jonas Quinn informs SGC that Naqahdriah is created in a catalytic reaction and the process is ongoing on Kelowna. If the reaction goes deep enough, heat and pressure will destabilize the Naqahdriah and it will blow the planet apart. Meanwhile, Jonas has been working with the brilliant young scientist Kianna, and have a mutual romantic attraction, but she is not what she seems.

Osiris has been visiting Jackson by night and using a mind control device to try and find the Lost City of the Ancients. SG-1 decide to attempt to capture her. However, Carter's new boyfriend Pete might get in the way.

The Alpha Site, where a prototype weapon to fight Anubis's supersoldier drones is being created, is attacked by a drone. Carter escapes but she is on her own and the drone is hunting her.

A film crew arrive at SGC to make a documentary but find their welcome less than enthusiastic.

Help is sent to rescue of an SG member who is unable to get to the gate. However, on the mission, a member of the SGC is killed.

SGC find the base of a rogue NID operation which has been attempting to mix the DNA of humans and Goa'uld, but all the agents except one have been killed.

A new President has been elected and must be briefed on the Stargate Program. However, as usual, the new Vice President Kinsey has his own agenda.

The SGC locates a Repository of Knowledge on P3X-439 and when Anubis attacks, O'Neill downloads their knowledge into his brain again. Finally, Bra'tac warns SG-1 that Anubis plans an attack on Earth. Hammond is replaced by Dr. Elizabeth Weir.

As Anubis' fleet arrives, SG-1 flies to Proclarush Taonas, a planet with an Ancient outpost and a ZPM. SG-1 locate another outpost in Antarctica back on Earth, from where O'Neill is able to destroy Anubis' fleet using the Ancient weapon.

Three System Lords meet with the SGC after their defeat of Anubis. Carter is abducted by Fifth. The Asgard's new homeworld Orilla is endangered.

O'Neill, with the help of the Asgard, is awakened and helps the Asgard in their fight with the Replicators using the knowledge of the Ancients that's still downloaded in his mind. Major Carter is released by Fifth. Jack is promoted to Brigadier General and replaces Weir as commander of the SGC.

An outbreak of disease is in fact the effect of possession by the ethereal remains of Anubis. Anubis escapes the SGC through the Stargate, though Carter alters his destination to a frozen, barren planet.

When SG-1 goes missing, Ba'al demands a ransom. After giving the SGC a booby-trapped ZPM, Camulus makes a deal to return to Ba'al on an assassination mission.

Tegalus is a world divided between two nuclear-armed nations engaged in a cold war: the Rand Protectorate and the Caledonian Federation, both of which possess a large arsenal of intercontinental ballistic missiles. When the SGC sends a MALP to Tegalus, religious fanatics who still worship the Goa'uld start a short-lived coup d'etat.

Teal'c is trapped in a virtual reality training machine that delivers electrical shocks when he fails his objectives. Daniel enters the game in an attempt to save Teal'c from cardiac arrest and together they fight against the increasing difficulty of the game.

Teal'c moves into an off-base apartment, where he becomes involved with his neighbor, Krista, who has an abusive boyfriend. Teal'c is accused of murdering the boyfriend and Daniel disappears while trying to prove Teal'c is innocent.

Alec Colson, the powerful leader of aerospace and biotech conglomerates, holds a press conference to announce that aliens exist, that they have already attacked Earth once, and that several governments are aware of this fact. Colson gives the governments involved 24 hours to tell the truth. When the time expires, he shows a living Asgard alien to the media.

Rya'c plans to marry a woman of the Hak'tyl, which makes Teal'c angry. Ishta brings the Hak'tyl to the SGC because they believe that their location has been compromised. Carter attempts to find a suitable planet for them. The Goa'uld Moloc captures Ishta on a planet named Goronak. Ultimately Moloc is killed by missiles from the SGC, but his forces are taken over by Ba'al.

Having recently acquired the Tok'ra symbiote poison, the Trust plan to steal the Stargate and eliminate the Jaffa. Teal'c tries to make a deal with the undercover Tok'ra Zarin on a planet designated P3S-114. The Trust captures Carter and brings her aboard the Alkesh where the Stargate is, but she's rescued by Daniel and Teal'c who beam aboard and use the Stargate respectively. SG-1 and the Stargate are beamed aboard Prometheus and measures are taken to ensure it never happens again, but the Trust escapes.

The crew of the Prometheus are incapacitated and removed, except Daniel, when it is hijacked by Vala, a pirate. Vala wishes to trade the ship for Naqahdah, but Daniel succeeds in retaking control of the ship and with the help of the crew in an Alkesh, fends off a Goa'uld attack that leaves Prometheus too badly damaged to finish the mission. Vala ultimately escapes in the end.

RepliCarter informs the SGC that Fifth has made all Replicators immune to O'Neill's disruptor, and promises to help them modify the weapon. In fact, her presence was needed to develop the immunity. She destroys Fifth and escapes to lead the replicators.

SG-1 finds that Harry Maybourne has become king on the planet where he took forced retirement. The planet is now under a Goa'uld threat, but Maybourne has found writings by a time-traveling Ancient that prophecy SG-1 will defeat the Goa'uld Ares. Ares sends Jaffa to the planet and comes in his mothership, but his forces are defeated by Daniel and Teal'c and his mothership is destroyed by O'Neill with the time traveling Puddle Jumper's weapons. Afterwards, Maybourne decides to remain on the planet with his people and his wives.

Russia and the United States reach DEFCON 1 because the Goa'uld may have compromised both governments via the Trust, which has been entirely assimilated. War is narrowly avoided when O'Neill convinces the Russian President of the truth and the Trust ship is destroyed by Prometheus, but the fate of Robert Kinsey is left unknown as he may or may not have been on the ship when it was destroyed.

Teal'c is preparing the Jaffa rebellion to capture the Holy planet Dakara, where the first larval Goa'uld implantation took place. Daniel is abducted by RepliCarter so she can discover the location of the Dakara Superweapon in his subconscious. Ba'al also moves his forces to Dakara by the order of Anubis.

Struggling with RepliCarter, Daniel halts the Replicators long enough for Samantha Carter, Jacob Carter, and Ba'al to use a combination of the device that dials every Stargate in the galaxy and the Dakara Superweapon to destroy all Replicators. RepliCarter kills Daniel Jackson.

Daniel Jackson must choose death or powerless Ascension whilst Anubis plans to end all life in the galaxy using the Dakara Superweapon - until Oma Desala stops him. Jacob Carter and Selmak are in trouble. Daniel is returned to human form on Earth.

An Indiana barber who carries the ATA Gene has his life ruined when, through an Ancient device, he begins to have visions of SG-1's missions. His life is given back to him when O'Neill informs his nearly-divorced wife of what had been going on.

SG-1 uses an Ancient Puddle Jumper to time-travel back to ancient Egypt to recover a ZPM. However, they cause Ra to take the Stargate at Giza with him when he leaves Earth, altering the future so the SGC doesn't exist.

An alternate-reality SG-1 must go back in time and fix the past to save the future. In the process, the team must re-recruit Teal'c and find the real Daniel Jackson, who is still in ancient Egypt. Alternate-timeline O'Neill and Carter express their love.

Lt. Colonel Cameron Mitchell is recruited by the SGC as leader of SG-1 but finds the original SG-1 has disbanded. Trying to find out how to bring them back together, Vala Mal Doran arrives with an artifact which could reveal an ancient treasure, and he finds this is his only opportunity to reunite the team.

After passing all of the tests found in Avalon, the makeshift SG-1 discovers the treasure, along with an Ancient long-range communication device. Hoping to find actual Ancients, Daniel and Vala are given control of the bodies of two people in a distant galaxy. Although... it's not what they expected.

When Daniel and Vala follow a mysterious man to find answers to their questions, they discover the Ori. The Ori, like the Ancients, are ascended beings, but pure evil entities that feel the need to be worshipped and have no rules to restrict themselves. Unknowingly through Daniel and Vala, the Ori know of life in another galaxy created by their long forgotten enemies, they begin to send their missionaries, Priors, through the Stargate. The first planet visited by a Prior in the Milky Way is P3X-421 and the SGC pays him a visit.

Hoping to disconnect the kor mak bracelets effects keeping them linked (Avalon), Daniel, Teal'c, Mitchell, and Vala try to pry the information out of the person she stole them from in the first place. When he wants something in return, they discover that his request isn't so easy to complete, and they must go on a series of quests to please his demands.

In order to steer the planet P8X-412 away from Origin, SG-1 is tricked by Vala into going to the planet she previously ruled as a Goa'uld. The inhabitants of the planet know nothing of the downfall of the parasites, and they believe that Vala is still their goddess, until a prior shows up, and attempts to expose her for who she is.

Samantha Carter returns to the SGC when the Ori seize control of a planet named Kallana as a foothold in the Milky Way Galaxy. After several attempts to halt the process, they discover that they have been helping the Ori achieve their goal, instead of foiling their efforts. The Ori have been building an enormous Stargate to allow their ships to enter the Milky Way, but they are stopped by Vala, who dies in the process, although there is a possibility that she got trapped in the Ori galaxy.

After Ba'al contacts Stargate Command, they learn he has been living on earth for several months as the head of a major corporation. His demands are that he is allowed to live in peace, or he will blow up a naqahdah bomb somewhere in America. Yet Gerak is determined to capture him... and takes a less subtle route. The bomb proves impossible to disarm, so Prometheus beams it into space where it detonates harmlessly, but Ba'al escapes with his many clones at his disposal.

A group of legendary Jaffa attacks SG-1 on a planet designated P9G-844 and captures Mitchell. While the rest of the team is forced to retreat, Mitchell is accused of killing one of the Jaffa. As punishment, he must square off against the slain Jaffa's brother, but he could be Mitchell's salvation.

SG-1 finds a man frozen in Ancient stasis on P3X-584, and brings him back to the SGC to find out his story. But when Daniel researches the laboratory where the man was found, he discovers that he was grown by Anubis to be a genetically advanced human.

When a disease breaks out across America, evidence leads it to be the Ori's doing. Preparing to track down a viable cure, an old friend (Orlin) takes on an unfamiliar human form to help out, but it might not be enough when the team's adverse ally joins the Ori.

While Orlin is working on a cure for the Prior plague, Mitchell and Daniel capture a Prior offworld to further the research of the antidote. Teal'c tries to stop Gerak, now a Prior, from corrupting the entire Jaffa Council towards Origin. Teal'c ultimately convinces Gerak to switch sides. Gerak cures the SGC of the plague, but it costs him his life. Thanks to Gerak's efforts and Orlin's work, a cure is found for everyone else, but Orlin now has brain damage and no memory of who he is and is put in a mental hospital.

SG-1 encounters the Galarans, a civilization that flourished under the umbrella of the Asgard Protected Planets Treaty, after centuries of Goa'uld domination. Due to the disengagement of the Asgard from the Milky Way, the Galarans have become concerned for their safety and developed a memory-grafting device, with which they hope to accelerate their technological development. They are eager to trade this technology with Earth in exchange for hyperdrive technology. After Mitchell's first dose of the memory-grafting device, he is accused of murder. Now the rest of the team must ally themselves with local scientists to prove his innocence.

Sixteen SG-1 teams show up, one after the other, at Stargate Command leading the 'real' team to conclude that they have each been inadvertently displaced from different parallel realities. One SG-1 team that arrives has Stargate Command's Dr Janet Frasier and the Tok'ra leader Martouf as members but they have been dead for two years in the current reality. The events are ultimately revealed to be a plan by the SG-1 team that first returned to Stargate Command (the 'Black Team') to steal Atlantis' ZPM, but the 'real' SG-1 foils them and sends everyone home.

Ba'al brainwashes members of the Jaffa High Council to thwart their move towards democracy. Cameron Mitchell faces a tough decision when he learns that an old friend is about to die.

The Rand Protectorate (Icon) converts to Origin and is rewarded with the design for a powerful satellite weapon, which they threaten to use against the Caledonians. When Prometheus tries to disable the satellite it is destroyed, although most of the crew escape to Caledonia. They are ultimately able to return to Earth through the planet's Stargate but after doing so, dialogue between Rand and Caledonia s break down and the two nations annihilate one another.

SG-1 is captured on an alien world after a deal with the Lucian Alliance goes bad ... and the planet's Stargate goes missing. SG-1 is rescued by the new Earth ship Odyssey and they go on a successful mission to retrieve all of the stolen Stargates from Ba'al.

The Ori have engineered a bioweapon of bugs (known as R-75 or Prior bugs), asexual, fast-reproducing, omnivorous insects. When given meat, its numbers increase dramatically and they become voracious swarming predators, able to strip a human to the bone in moments. They prefer darkness and spend most of their time underground, where they hunt via echolocation. When a group of Earth diplomats go on a tour on the off-world Gamma Site research base, R-75 overrun the base and consume most of the base personnel. Cut off from the Stargate, SG-1 is forced to flee to a research site and set up a message to alert the Odyssey to rescue them when it arrives. The Odyssey rescues SG-1 and the delegates and destroys the bugs with a toxin, but the bugs are spreading on other planets and are revealed to be another tactic of the Priors in submitting the people of the galaxy in worshipping the Ori.

Mitchell and Carter are shifted to another dimension, making them invisible to everyone at the SGC. Teal'c and SG-12 discover that the Sodan have been brutally attacked.

Vala Mal Doran makes contact with Stargate Command from the Ori home galaxy, and tells the story of her life undercover in a village of followers building the Ori's invasion fleet and her mysterious pregnancy. She ultimately joins an anti-Ori resistance movement with plans to destroy the fleet, but the plan fails and Vala is nearly killed by her husband Tomin before she convinces him to spare her and take her with him to war in the Milky Way galaxy.

SG-1 discovers the village of Camelot on PX1-767 and must face Merlin's security system when they go in search of an Ancient weapon. The Ori invasion begins. A fleet composed of ships from all over the Milky Way made up of the Earth ships Odyssey and Korelev along with ships from the Free Jaffa, Tok'ra, Lucian Alliance as well as one Asgard ship. The fleet faces off against four Ori ships and are decimated with the Korelev destroyed with Daniel and Mitchell on board. Vala, on board one of the ships, can only watch the devastation in horror as she starts to go into labor.

Following their devastating attack on Milky Way forces, the Ori leave the scene to begin their holy crusade and purify the galaxy of evil. As the remnants of the makeshift Milky Way fleet come together, Vala gives birth to a baby girl, the Orici, genetically altered by the Ori to command their forces. Daniel Jackson has escaped to the Ori flagship, which has just arrived on Chulak to convert the Jaffa into believing in Origin. He pretends to be an Ori warrior while he and Vala attempt to kidnap the Orici, who has been named Adria by Vala. An attempt by SG-1 and Bra'tac to destroy the fleet over Chulak fails and Bra'tac sets a collision course with one of the ships in a futile attempt to destroy it while Daniel is captured by Tomin, Vala's husband. He escapes and knocks out both Adria and Tomin, but is disarmed by a Prior and trapped with Vala in a wall of fire with no way out. In the nick of time, the Odyssey arrives and beams SG-1 off their ship and Daniel out of the Ori warship. As Daniel beams out, he manages to grab Vala and take her with him, but leaves Adria behind.

Questing for the Sangraal, the team ends up in a mess of trouble when they are struck with a sleeping sickness on Vagonbrei (aka Verus Gen Bree), one of the three planets that the weapon is supposed to be on. Meanwhile, Landry must decide whether or not Vala can be trusted to remain at the SGC as a possible future member of SG-1, but it might not be up to him when the IOA steps in. In the end, Teal'c discovers a lizard immune to the parasite causing the sickness and a cure is reverse engineered from it. Vala is accepted as a provisional member of the SGC, though she is not allowed to join SG-1 officially yet.

SG-1 visits Atlantis (Stargate) with two goals: to find new clues about the location of Merlin's superweapon, the Sangraal and to disable the Supergate (Stargate) by connecting it to a black hole in the hope that they can stop the Ori from sending more ships through. As Dr. Rodney McKay (David Hewlett), Chief Science Officer of the Expedition assists Sam and Mitchell in their elaborate plan to jump a wormhole by sending a bomb directly into the Supergate using the Odyssey. Daniel, Vala and Dr. Elizabeth Weir, the head of the Expedition search the city's databases for information, eventually confronting the Ancient known as Morgan Le Fey. Morgan shows them the address of the two other planets they need to search but when she tries to tell them something important, she is pulled away by the other Ancients. At the same time, the Odyssey succeeds in its mission, destroying both a Wraith Hive Ship and an Ori warship at the same time.

When an Al'kesh crashes only a few miles away from Cheyenne Mountain, the team finds Ba'al, and he asks them to capture his rebellious clones; in exchange, he offers information about the whereabouts of Merlin's weapon. As the clones are brought in for questioning, SG-1 must determine which Ba'al is the real one. Eventually the Ba'als take over the SGC in order to get the SGC's list of Stargate addresses, which includes addresses known only to the Ancients, in order to find Merlin's weapon. The Ba'als get the addresses and beam out to a ship in orbit while SG-1 realize Ba'al brainwashed Agent Malcolm Barrett to help him escape.

The team discovers several creatures that only appear on worlds where the SGC has used the Sodan cloaking devices. Things get worse when another creature appears in the woods on Earth where Mitchell and Landry are spending some quality time at O'Neill's cabin. Coming together, SG-1 and Landry kill the creature and another one that appears and close off the area even though they're sure they got them all. With the creatures dead, the team and Landry relax together at the cabin.

Martin Lloyd contacts the SGC, looking for their assistance in writing a feature movie to follow up Wormhole X-treme, allowing the audience to see some of the team's most creative fantasies. It also marks Colonel Mitchell's 200th time through the event horizon, and is the 200th episode in the series. In the end, SG-1 go on what appears to be a routine mission and are joined by Generals Landry and O'Neill and Sergeant Walter Harriman. While the Womhole X-treme movie is cancelled, the series is renewed and survives ten more years.

Deadly battles erupt between the Ori, led by Adria, and the Jaffa, after 100,000 villagers are wiped out by a powerful energy wave which Adria believes was SG-1's doing. She captures Daniel and Vala and uses her powers against them to determine the nature of the weapon. Adria learns about the Dakara superweapon and heads there to destroy it. SG-1 are rescued by the Odyssey, but Dakara and its weapon are decimated, fracturing the Free Jaffa Nation.

During a dinner out, Vala is captured by the Goa'uld Athena, where she attempts to pry memories out of Vala's subconscious during her time as a host. When things go wrong, Vala develops amnesia and runs away and she must begin to piece herself back together. SG-1 eventually catches up to her and she tries to run again, but Daniel manages to get her to remember him at least and she returns to the SGC where she recovers her entire memory and finally achieves her dream of becoming a fully-fledged member of SG-1.

After the Odyssey, and most of SG-1, are attacked and captured by the Lucian Alliance and the Odyssey is hijacked, Mitchell must infiltrate the organization to save his friends from being caught in the crossfire in a deadly Lucian Alliance civil war, but the situation may quickly go awry. Eventually Vala and Daniel manage to retake the Odyssey and thanks to Mitchell's efforts, are able to get enough time to repair the hyperdrive and escape after beaming Mitchell and Teal'c aboard. Earth is now officially at war with the Lucian Alliance. But the mission is overwhelmed by the murder of Colonel Paul Emerson.

Following a dream Vala has, SG-1 searches a planet whose address is made up of the three addresses that Arthur and his knights searched for Merlin's weapon. On the planet, they discover that Ba'al is also there and are forced to work with him and Adria to locate the weapon with each group having differing objectives. Together the group passes a series of tests left by Morgan Le Fay, but are confronted by a dragon...

After defeating the dragon, SG-1 and Ba'al are transported to a series of planets where they discover a laboratory and Merlin in stasis. Realizing that the anti-Ori weapon has been destroyed but that Merlin can rebuild it, the team awakens him and he agrees to build a new weapon but dies before he can finish. Daniel downloads Merlin's consciousness and continues building the weapon while Carter and Ba'al work on fixing the Stargate so they can escape. Before Daniel can finish the weapon, Adria, who was left behind, arrives with her forces to stop them. Daniel takes out the soldiers with Merlin's powers and holds Adria off so the rest of SG-1 can escape, but Daniel is captured by Adria and Ba'al is killed.

In an attempt to utilize Merlin's phase shifting technology, SG-1 answers the cry of a village pressured by Origin, and they attempt to phase shift the entire area. The plan appears to have been successful, until the device fails, and the Ori forces begin their onslaught. Meanwhile, Tomin, ordered to convert Vala to Origin, begins to question his faith in the religion when his views on the Ori's teachings clash with those of the Prior leading the assault, who's using the teachings to justify his actions. In the end, Mitchell and seriously injured Carter manage to bring the entire village out of phase using the power source of an Ori staff weapon, making it seem like the Ori have destroyed it. Tomin helps Vala escape even though he knows it may cost him his life.

Carter experiments with Arthur's Mantle even further, but her studies send her to an alternate universe where the Ori are only hours away from obliterating the planet and the Stargate Program has been made public, resulting in martial law being spread across the U.S. In order to return home, Carter must help, but when things finally seem to go her way, President Landry won't allow Carter to return. Carter succeeds in saving the alternate Earth by shifting it out of phase and eventually convinces Landry to let her go by telling him about his counterpart from her world. Carter returns after two weeks absence with the help of Rodney McKay (David Hewlett) and is amused to discover that her team has spent that time talking to an empty room. However, there is still no sign of Daniel.

When SG-1 discovers a village tempted by Origin without any threats of destruction, they're in for a huge shock when they find out that their own teammate, Daniel Jackson, has been turned into a Prior of the Ori. The team captures Daniel who reveals that he and Merlin have been plotting the destruction of the Ori and need their help to finish the job. The team and O'Neill are skeptical as Daniel's plan calls for reopening the Supergate which would let through more Ori ships, but decide to do the plan themselves while Daniel is put into stasis. Frustrated, Daniel breaks free, hijacks the Odyssey and kidnaps O'Neill. Daniel and O'Neill arrive to find that Adria and her forces have captured SG-1, but Daniel is able to overpower Adria. With Daniel in command of the Ori ship, O'Neill shuts down the Supergate and Daniel flies the ship through as Vala finishes and activates Merlin's weapon. At the last moment, O'Neill beams the team off the ship, but Adria is left behind. Due to Merlin's modifications to his body, Daniel reverts to his normal self with Merlin gone as well, but it is unclear if the Ori are dead or not. Also, six new Ori warships come through the reopened Supergate.

After SG-1 destroys a Lucian Alliance shipment of kassa (a crop containing a highly addictive stimulant) shipment near the planet Rolan, the Lucian Alliance places a bounty on all of the members of the team, threatening national security and lives. Meanwhile, Mitchell returns to his hometown for a high school reunion, accompanied by Vala... and bounty hunters hot on their trail. SG-1 manage to dispatch most of the bounty hunters and convince the last to go after Netan, the leader of Lucian Alliance and he apparently kills him.

Searching for a great treasure, the team gates to a planet where they discover that the DHD is a prop in an exhibit, in turn, when they ask for help they appear to have come out of nowhere. Now SG-1's mistaken for hostage-taking rebels and they are forced to play the part in order to survive. Things degenerate as the team tries to hold off the authorities long enough for Stargate Command to make contact and send them a power source capable of dialing the Stargate, but Vala discovers a naquadah bomb which she is able to use to power the Stargate. As the team tries to return to Earth, they are apprehended by the authorities, but Mitchell is able to convince them to let SG-1 go. However, the people of the planet apparently bury the Stargate afterwards.

A former foe of Teal'c's has turned to the way of Origin and bombed a Jaffa summit on a Jaffa world named Dar Eshkalon attempting to rekindle the council. The aftermath appears to have killed many Jaffa, and leaves Bra'tac hanging on to his life. Enraged at what has happened and seeking revenge, Teal'c now decides to go on a single-minded quest... and it seems that not even SG-1's actions can stop him from achieving his goal. Teal'c ultimately tracks down his old foe and finally kills him, despite being seriously injured in the process.

Vala's father, Jacek, makes a deal with the SGC for sanctuary in exchange for helping stop an attack on Earth. As Jacek attempts to repair his relationship with Vala, General Landry is inspired to reach out to his daughter, Dr Lam, and his ex-wife. With Jacek's information, SG-1 and the Odyssey are able to track down and destroy a fleet of ships poised to bomb Earth, but discover Jacek double-dealing to steal the naquadah on one of the ships already on Earth. SG-1 outcon Jacek and capture the ship while Jacek flees in a fake and peddles off the styrofoam peanuts left on the ship instead of naquadah.

In an attempt to capture Adria, the team uses Vala as bait, only to have Ba'al beam the Orici away in SG-1's time of victory. When they track down the parasite, they discover Ba'al wants to end the reign of the Ori just as much as the SGC, and he's taken a drastic course of action to do so, implanting Adria with one of his cloned symbiotes. The symbiote is ultimately removed and eventually killed, but Ba'al fatally poisons Adria beforehand and in order to survive she ascends.

The Asgard summons SG-1 to tell them that their experiments to halt their genetic degeneration have failed, meaning they are a dying race. Because of this, the Asgard have decided to give everything [they] have and know to the Tau'ri. Thor tells Colonel Carter that the people of Earth are the fifth race, the other four being the Ancients, Nox, Furlings, and the Asgard. When the Ori show up, the Asgard destroys Orilla, and themselves with it, so that their technology does not fall into the hands of the Ori. With the new weapons the Asgard equipped the Odyssey with, they are able to destroy an Ori mothership with ease, but come under repeated assault from two more who chase them wherever they go. In a desperate attempt to stop the relentless pursuit, SG-1 and General Landry beam the crew off the ship onto an uninhabited planet and lock the ship in a time-dilation field when they are unable to separate the new upgrades from the hyper drive. They end up spending around fifty to sixty years trapped on the ship, moments away from death if they ever stop the field. During that time, Landry dies and Daniel and Vala get together. As an old woman, Carter figures out how to reverse time so this never happens, but unless someone stays old, everything will happen the same way. It also requires temporarily allowing the ship to be destroyed to allow an energy blast to power the effect. Due to his greater lifespan, Teal'c volunteers and is able to give Carter what she needs to separate the hyper drive quickly and the Odyssey escapes.

SG-1 discovers a box that they believe contains the Ark of Truth while digging on Dakara, but before they can open it, Ori soldiers arrive, led by Tomin. Daniel tricks them into opening the box, but it is revealed to be a fake. When Tomin is ordered by a Prior to kill them, he refuses, and Mitchell kills the Prior, whose powers were being blocked by the Anti-Prior device. Shocked at the death of their Prior, the Ori soldiers surrender.

Back on Earth, General Landry and Mitchell meet James Marrick, an IOA representative sent to interrogate Tomin. When Daniel Jackson realizes that the Ark is still in the Ori galaxy, Marrick is assigned to accompany them on board the Odyssey through the Supergate. In the Ori galaxy, a member of the anti-Ori resistance tells the team that according to legend, the Ark is on Celestis, the Ori capital. When SG-1 beams down to the planet, Marrick activates the Asgard computer core which alerts the Ori to the ship's location.

Mitchell and Carter beam back to the Odyssey and discover that Marrick has used the core to build a Replicator, intending to plant it on an Ori ship and let it spread to their entire fleet. When Mitchell attempts to destroy it with an anti-Replicator Gun, the replicator escapes, and Marrick reveals that the IOA removed that weakness from the design, although conventional weapons are sufficient to destroy individual replicators. Marrick implies that a shutdown code has been included as a failsafe, but claims he does not know what it is. He is placed in the ship's brig. With several Ori ships approaching, Mitchell attempts to beam Daniel, Teal'c, Vala, and Tomin up from the planet, but the replicator takes over the system and keeps Mitchell from doing so. With no other option, the Odyssey jumps to hyperspace to escape, leaving the others on the planet.

Daniel finds the Ark in a set of catacombs, and after several ground tremors, brings it to the surface. When the team emerges, they are ambushed by Ori warriors, and Teal'c is shot in the back while the others are captured. When they are brought to the city, Vala discovers that the Ori were indeed killed by the Sangraal during the events of The Shroud. Adria has ascended and taken over all of their power. Teal'c, who has been walking toward the city of Celestis since he was shot, collapses due to his wound within sight of the city. He is subsequently revived by Morgan le Fay and continues on to free Daniel. Morgan then arrives in Daniel's cell (initially in the guise of Merlin) and tells him if he can expose one Prior to the Ark, the others will be turned by a link in their staffs. This will weaken Adria enough for Morgan to stalemate her.

In the meantime, a Prior arrives on Earth, offering a last chance to convert to Origin. When General Landry refuses to even listen to him, the Apollo detects a fleet of Ori motherships waiting on the edge of the solar system. On the Odyssey, Marrick is attacked by Replicators who infest his body. In the ensuing battle, Mitchell is able to briefly disable the Replicator connection to Marrick's brain who then informs Mitchell the shutdown code for the Replicators is located on the other side of the crystal used to create them. Mitchell activates an explosive charge which kills Marrick. Mitchell informs Carter who activates the shut-down command, deactivating the Replicators.

When the Ark is activated and opened, the Doci is caught by the beam and made to see that the Ori are not gods and spreads this belief to all of the Priors in the Ori galaxy and through them their followers. With Adria now in a weakened state, Morgan is able to engage her in an eternal battle. SG-1 exposes the Prior on Earth to the Ark, transmitting the knowledge about the Ori to all of the Priors in the Milky Way, and thus turning all known Priors in the Universe.

In the aftermath, Tomin departs for the Ori galaxy as the new leader of his people, he and Vala agreeing that, while the Ori themselves were liars, Origin itself has a worthwhile message. Tomin asks Vala to come with him, but Vala apologizes and says that she feels her place is with the SGC. Over Daniel's objections the Ark is taken to Area 51 for study.

SG-1 and Jack O'Neill attend a Tok'ra extraction ceremony for Ba'al, the last of the Goa'uld System Lords. He gloats that he is merely the last clone and that the real Ba'al has a fail-safe plan. The real Ba'al travels back in time to 1939 Earth and massacres the crew of the Achilles, the ship carrying the Stargate to the United States; the captain survives long enough to keep the ship from being destroyed. In the present, people and objects disappear, including Vala Mal Doran and Teal'c. Jack is killed by Ba'al before Samantha Carter, Daniel Jackson and Cameron Mitchell reach the Stargate. They emerge inside the derelict Achilles, which has drifted to the Arctic — Ba'al's actions have created a timeline in which the Stargate Program never happened. After escaping from the sinking Achilles, they are rescued by a team led by Colonel Jack O'Neill. Although General Landry believes their story, they are denied permission to change the timeline. In the alternate timeline Daniel is still trying to convince people about his theories of the pyramids, Carter died in a space shuttle accident and Mitchell does not exist at all because his grandfather was the Achilles captain. The three are separated and given new lives to lead.

A year passes, and SG-1 is called back into action when Goa'uld scoutships appear. Ba'al has defeated the System Lords and now stands ready to conquer Earth, with Qetesh, still residing in Vala's body, as his Queen and Teal'c as his First Prime. SG-1 is brought to President Henry Hayes and General George Hammond, who inform them that, based on SG-1's accounts, they have recovered the Antarctic Stargate and are excavating the Antarctic Ancient outpost. SG-1 is sent in F-15s to McMurdo Station to gate to Proclarush Taonas, another Ancient outpost, to retrieve a Zero Point Module to power the Antarctic outpost. Above Earth, Ba'al's armada arrives. To the displeasure of his lieutenants, all former System Lords, Ba'al announces that he will treat the Tau'ri leniently. Suspicious about Ba'al's knowledge of Earth, Qetesh betrays him and forces him to tell her everything. She has her ships destroy McMurdo and the Ancient outpost, and she kills Ba'al after Teal'c discovers her treachery. As Teal'c escapes to an Al'kesh, Qetesh orders the fleet to bombard Earth while she goes to secure Ba'al's time machine.

Amidst the massive Goa'uld attack, SG-1 is rerouted to Russia, as the Russians had retrieved the Achilles' Stargate from the ocean floor. Teal'c arrives at the facility as well, seeking to use the Stargate to reach the time machine before Qetesh. The two sides form a truce and arrive together at Ba'al's time machine: a vast underground supercomputer connected to hundreds of satellites that monitor solar flares that could intersect the wormhole formed by the Stargate. SG-1 must wait for the right flare with which to journey to the past, but an attack by Qetesh's troops forces them to dial Earth in the year 1929 - ten years before their target date. Sam and Daniel are killed in the firefight, and only Mitchell reaches the Stargate before Teal'c, mortally wounded, destroys the time machine along with himself and Qetesh. After a decade of waiting, an older Mitchell stows away on the Achilles and kills Ba'al and his troops when they come through the Stargate. In the present of the now-restored timeline, SG-1, completely unaware of the previous events, watch the extraction proceed without incident. On Earth, Daniel wonders what Ba'al meant by his fail-safe, but they decide not to dwell on it.

After relinquishing her position at Stargate Command, Dr. Elizabeth Weir has been working in the Antarctic Outpost, gathering members of an expedition to embark to the lost city of Atlantis. When they seem to be able to ascertain a gate address, a new adventure begins.

After Sheppard's return with refugees from Athos, Atlantis, moments away from being crushed, breaks away from the ocean floor, rising to the surface just before the shield fails. Now, given a chance to rescue his people, Sheppard needs to make Weir see things his way.

Eager to experiment with new technology, Dr. McKay volunteers to be Dr. Beckett's first patient for his new ATA gene therapy. Now able to use a personal shield emitter, McKay recklessly tests its properties, only to find that it could lead to his death. Elsewhere, a living shadow entity threatens the city after it was accidentally released from a container where the Ancients were studying it. It roams the city looking for energy to feed on, and the more it feeds, the more lethal it becomes. Finally members of the Atlantis expedition manage to send it to planet M4X-337.

Needing medical attention, Sheppard's puddle jumper races to Atlantis, only to become lodged in the Stargate. Now, they only have 38 minutes until the stargate automatically dis-engages, and the jumper gets cut in two... leaving them to asphyxiate in outer space. (First appearance of Radek Zelenka, David Nykl)

When the offworld teams are attacked one time too many, Dr. Weir must consider that there is an Athosian spy in their midst, but upon further investigation, all evidence points to Teyla. Feeling betrayed, the Athosians resettle to the newly-discovered mainland.

The team visits M7G-677, a primitive world where no one is over 24 years old, because of ritual suicides they believe keep the Wraith at bay. McKay discovers that they are in fact being protected by an Ancient electromagnetic shield. He takes the ZPM powering it, unwittingly allowing a long-dormant Wraith transmitter to reactivate.

On planet Hoff, Dr. Beckett helps the Hoffans, humans who are developing a vaccine against the Wraith, complete the drug. Despite a 50% mortality rate and a warning from the Atlanteans that the Wraith are likely to destroy them as a potential threat, the Hoffans elect to take the drug.

In order to keep the expedition fed, the team visits the Genii to trade for food. Although Teyla believed them to be peaceful farmers, Sheppard and McKay find an underground bunker, letting them see the real face of the Genii.

When Atlantis discovers M5S-224, a planet that will allow them to gate to Earth, they return under the guise they will be able to go back to the city, due to the new hyperdrive on the Prometheus. Yet, when the engines explode, the team begins to question the mystery of their situation.

Exploring the planet, Sheppard and Teyla discover a colossal storm with the ability to crush the city in its current state. The Manarians (first mentioned in Underground) give shelter to most of the Atlantis Expedition. McKay and Zelenka think of a daring way to power up the shield, but it's no coincidence that the Genii invade the city at their weakest moment. (First appearance of Acastus Kolya, Robert Davi)

As Sheppard attempts to reclaim the city from the Genii, who still have Weir and McKay as hostages, the bulk of the storm fast approaches. Now, the rest of the team must take drastic measures to help wherever they can, before there is nothing left to save.

Sheppard and McKay lead two scientists to survey an Ancient orbital defense platform discovered from the city's sensors. When they arrive via jumper, they find a Wraith distress beacon emanating from the nearest planet's surface... and are in for an unusual surprise.

Inspecting the city for storm damage, a party of scientists unleash a virus that causes hallucinations and eventually... death. Now, nearly a third of Atlantis' residents have been infected, forcing a lockdown. It's up to Sheppard to keep it from spreading, and eliminate it for good.

Searching a new planet, the Wraith find the team, only for them to be shot down by a mysterious weapon. On the surface, they find a primitive world named Proculus that would make ideal sanctuary for those fleeing from the Wraith. But the inhabitants believe their goddess won't permit it.

While exploring the city, the team stumbles upon a stasis unit holding an extremely old woman, who they believe to be an Ancient. When they revive her, she claims to be Dr. Elizabeth Weir, and she has a story she's been waiting ten thousand years to tell.

The team searches for a Zero Point Module rumored to be hidden on the planet Dagan, an old Lantean outpost. The ancestors of the Daganians, the Sudarians, were entrusted with a ZPM some 10,000 years ago. In attempt to locate and excavate the ZPM, the team crosses paths with Kolya once more, but it's not the only thing to worry about when their new allies have motives of their own.

With the Wraith fast approaching to claim the city, Atlantis must somehow send a message back to Earth for a desperate attempt in survival. Meanwhile, Sheppard and Teyla go offworld to try to find more intel on the Wraith fleet, but end up with a few hitchhikers.

Plagued by terrifying nightmares, Teyla tries to dive into her past offworld, where she finds an abandoned Wraith lab. Bringing back the findings, Dr. Beckett makes a surprising discovery in her DNA makeup, leading to a possible way to gather information from their enemy.

McKay leads a team to activate the Ancients' orbital weapons platform to destroy the hive ships on the final stretch to the city. After the team has found a potential Atlantis Alpha Site (M1K-439 as Planet Waterfall, the Tyrannosaurus-like planet M1M-316, the Genii-infested M4H-212, and M85-393 with intense daytime temperatures were rejected), the city's personnel are preparing for evacuation, when they discover the kamikaze dart pilot (The Brotherhood) has survived in the city.

As a response to the message the expedition sent, the SGC sends Atlantis reinforcements via ZPM. Now the Ancient power source is en route through the latest Earth battleship, the Daedalus, and they need to hold out for four days, or Atlantis risks destruction.

The timely arrival of the Daedalus, led by Col. Steven Caldwell, saves Maj. Sheppard's life from a suicide bombing run. Atlantis wins the first round against the wraith and therefore think they are safe for the moment, but then they discover that a lot more hive ships are on their way to Atlantis. Thankfully, with the new ZPM, McKay might pull off another miracle. (First appearance of Colonel Steven Caldwell, Mitch Pileggi)

Strange malfunctions begin to occur when newley promoted Lt. Col. Sheppard along with other members of the expedition return from a trip to Earth aboard the Daedalus. When things go too far, they discover that the ship has been infected by a Wraith virus, and now it has the instinct to stay alive, even if it means it has to kill in order to survive. Meanwhile perodic flashbacks reveal the events of their visit to earth including a meeting with Ford's cousin.

Following a lead on the whereabouts of Lt. Ford, Lt. Col. Sheppard and Teyla get captured on P3M-736 by Ronon Dex, a man who they find out is a runner, hunted by the Wraith. When they offer to help, the team must face off against their old ally, and in the process possibly gain a new one.

On Planet Thenora after the team witnesses the aftermath of a culling, a Wraith Dart suddenly appears. When it's shot down to preserve Atlantis' secret, they discover that McKay and a female marine officer were beamed aboard, whilst their drastic measures to save them has left the consciousness of the female marine officer trapped in Dr. McKay's body.

Sheppard's team stumbles upon a technologically advanced society, the Olesians, on planet Olesia who purposely leave their criminals on a penal colony near the Stargate, for the Wraith to discover them first. But after the prisoners shoot the jumper down, they discover that this punishment is too effective and the crime rate drops, forcing the Olesians to start sentencing petty criminals and innocent people to the Wraith.

After having found an experimental Ancient power generator, McKay becomes obsessed with triumphing where the Ancients failed, but the price might be too high. Elsewhere, Teyla and Ronon travel to the planet Balkan, to trade, but discover that not all of Ronon's people died.

While investigating a planet, the team comes across a Wraith girl who has been raised by her human father, hiding from the people of the nearby village in fear of her life. But she doesn't consider the consequences when she takes an incomplete drug to turn herself human.

After Ellia (the Wraith girl from Instinct) injects Sheppard with the retro-virus (Instinct), the Atlantis team races against time to find a way to reverse his transformation into an Iratus bug hybrid. But even though he might make it difficult for them, he could be the key to his own salvation.

The team finds an Ancient warship still inhabited by Ancients in suspended animation. They are all connected together through a virtual environment, that Sheppard enters to communicate with them. The only problem being, the Ancients think that their virtual lives are reality and they have an unexpected enemy in their midst.

Sheppard's team is kidnapped off-world, only to find that their captor is none other than Aiden Ford. He has recruited several men into taking the Wraith enzyme, and now they intend to use the team to destroy a Hive Ship to prove the glorious effects of the drug.

After the attempt to destroy the Hive backfires, the team is captured by the Wraith and Sheppard finds himself up against the Wraith Queen who is demanding answers. Meanwhile, Dr. McKay takes a massive dose of enzyme and escapes to Atlantis in a state of frenzy, but his choice could put him on the edge of death.

Sheppard gets pulled into an Ancient device, separating him from the rest of his team and the outside world. While trying to get him out, the team discovers that time moves much more quickly where Sheppard is and he could die of old age before they release him.

It is discovered that The Trust have infiltrated Atlantis and planted a bomb inside, set to go off the next time they dial Earth. To add to the tension, two Wraith cruisers are on the way, and Dr. Weir wants to figure out if there could be a Goa'uld spy in Atlantis' midst.

During the test run of a recently repaired puddle jumper, it crashes deep into the ocean, leaving Dr. McKay sinking underwater. When he shows the first signs of losing hope (and sanity), he must rely on a hallucination of Lt. Col. Samantha Carter for his survival.

The team finds a world that possesses Ancient technology, but only the royal family may be allowed to operate it and lowly villagers are treated with little dignity. When he tries to set things right, Sheppard finds himself a pawn in the rivalry between the heirs to the throne.

After recovering two alien stasis pods from space, the minds of the inhabitants are transferred into Dr. Weir and Sheppard. But when it's discovered that the two are in fact enemies hoping to settle an ancient score by killing each other once and for all, they put the entire population of Atlantis in danger.

Ladon Radim comes to the expedition wanting to overthrow the Genii leader, Cowen. They are reluctant to help, but it seems he has discovered a ZPM that he could trade with the expedition. The Genii set a trap for the Atlantis team on a ruined planet, M6R-867, and Radim's true motives are revealed.

An amnesiac young Lieutenant in Atlantis, Michael Kenmore, suffers poor treatment from the personnel, and disturbing nightmares that he is a Wraith. Yet things become worse, when he accidentally stumbles upon a shocking discovery about himself... he is one. (First appearance of Michael Kenmore, Connor Trinneer)

The team comes to aid a low-level technological civilization, the Taranians, taking refuge throughout an Ancient outpost. While trying to repair systems, McKay discovers a supervolcano below the outpost that will obliterate life on the entire planet of Taranis, suggesting evacuation to a new planet. Yet during the evacuation process, the Stargate is swallowed up by the supervolcano.

A Wraith faction (including Michael) contacts Atlantis to seek help in destroying their common enemies, the Wraith. Because the Wraith are currently engaged in a destructive civil war, they suggest using Atlantis' retro-virus to turn their native foes into human prey.

After the Wraith betrayed the expedition (Allies), they head to Earth with McKay and Ronon. Meanwhile, Elizabeth must answer to the IOA because of her actions during the short-lived alliance, and Sheppard must stop the hive ships from reaching Earth, whatever the cost. This episode sees the first appearance in the show of Robert Picardo as Richard Woolsey, a character first seen in Stargate SG-1.

After using the retro-virus to turn an entire hive into humans, they create a Stargate-less colony for them to live in until a more permanent solution can be found. All the while, Richard Woolsey, newly arrived at Atlantis, observes Dr Weir to determine whether she's fit to continue to lead the expedition.

The Atlantis team encounters a village that adore one man named Lucius Lavin (Richard Kind) to the point of insanity. He claims to have medicines (found on M6H-491) to offer the team, but when Beckett investigates, he brings the man back to Atlantis smitten by the man's charm. Soon, the entire expedition falls under his spell.

When Ronon becomes a prisoner offworld, his captors hand him over to the Wraith, who take him to his homeworld. There, he is forced to once again become their prey, but witness to his capture, Sheppard's team races to Sateda to return him to his new home.

Weir and the team visit M7R-227, a planet where an advanced civilization lives who split off from the Lanteans thousands of years ago, and have built an entire planet out of Ancient technology. But after their adverse behavior, they soon discover they might not be Lantean or even organic for that matter.

Dr. Weir awakens in a sanitarium outside of D.C. only to find that Atlantis, and the Stargate Program, was a fantasy. But after a series of nightmarish visions, she doesn't take long to realize things aren't what they appear to be, and she is determined to return to the city.

Sheppard is captured by Kolya, who plans to trade him for Ladon Radim. To help persuade Dr. Weir, he uses his captured Wraith to feed off Sheppard over and over again. To escape, Sheppard must find common ground with the only one who wants to achieve the same goal. (Introduces Todd played by Christopher Heyerdahl)

On Earth, a young housewife has written a ground-breaking proof that could benefit Atlantis. She is McKay's sister who has given up a career as a scientist to raise a family, and when he persuades her to come to Atlantis, another Rodney comes from an alternate reality.

Trying to locate a missing team, Sheppard's team finds a Wraith hallucinatory device on M1B-129, and after a few hours of research, McKay deems it to be a threat for everyone's safety. Yet, while attempting to leave, the DHD explodes, leaving them to become victim to the device.

During the first test of the intergalactic bridge, the Daedalus discovers an Ancient Warship between the two galaxies. Rescuing the residents on-board, the team is shocked, when they learn that the Ancients want the expedition gone, forcing exodus back to Earth.

When the Asurans take the city under Ancient command, O'Neill and Woolsey are captured in the crossfire, forcing the team to disobey orders and return to the Pegasus Galaxy. Reuniting with Teyla and Ronon, they must reclaim Atlantis without destroying it in the process.

Everyone starts to see ghosts of Lanteans, caused by echoes being emitted by whale-like creatures (Flagisalis, first encountered in Grace Under Pressure) converging on the city. When side effects begin to occur, McKay discovers that the Ancients tried to teach the whales their language, who now try to warn them about a natural disaster that endangers all life on the planet.

Lucius Lavin (Irresistible), is up to his old tricks again, he's using an Ancient Personal Shield Emitter (Hide and Seek) to pose as an invincible hero, but needs the team's help when Acastus Kolya shows up to deal with Lavin personally. (Final appearance of Acastus Kolya, Robert Davie)

After an Ancient device within the city alters Rodney's DNA, he gains superhuman powers. Although he initially takes them as a blessing, his enhanced brilliance is checked only by his impending death... unless he learns to overcome his ego to ascend.

Major Lorne's team discovers a planet that fits the description of Lt. Col. Sheppard and Dr. McKay's competitive video game. It turns out that, through a series of Ancient satellites above planet M4D-058, the game has been controlling real people, the People of Geldar and Hallona, who now stand on the brink of war and destruction.

Colonel Sheppard's team discovers a space station where the last of a race of humans remain. They soon discover, however, the entire population is in danger when the station is damaged through the suicide of a recently awoken resident.

The expedition tries to relax during a mandatory day off, until an unexpected explosion leaves three people dead, and reveals that one other scientist is a walking time bomb. Unfortunately, the attempt to resolve the issue will result in the loss of an important face in Atlantis.

The team discovers a drill platform at the bottom of the ocean which may be an alternative to ZPMs, but during their visit, they are ambushed by an old Wraith Queen. Once they capture her, Teyla's desire to get information could lead her down a dangerous path.

Now that the Wraith see Michael as an unclean thing, he has been experimenting with Iratus bugs, creating monsters for an army to rule the galaxy. When the team stumbles on one of his labs, they are in for a world of hurt when they are attacked by countless creatures, experiments that Michael himself can no longer control.

When the Apollo arrives, they launch a preemptive strike against the Asurans when it is discovered that they are building a fleet of ships but later a weapons satellite appears above the city, firing a beam at Atlantis which leaves everyone trapped in the city and the Expedition unable to use their Stargate. Ronon, Rodney and Teyla are left injured and Elizabeth fights for her life when the beam strikes the Control Room. The episode ends with Atlantis stuck floating helplessly in space due to the hyperspace shutting down and they only have 24 hours of power left before the shields fail and everyone dies.

Escaping from the Replicators satellite weapon, Atlantis encounters further problems as the city's shield begins to severely deplete their over-taxed ZPM. With limited resources, the team undertake a myriad of repairs, whilst Dr McKay and Dr Keller are forced to make a tough decision when Elizabeth Weir is injured.

Colonel Sheppard's team and Dr Weir plan a daring infiltration of the Asuran homeworld to steal a ZPM from the Replicators, in order to power up Atlantis and head to their new home. Dr Weir's new powers convince Rodney that he can upload a new attack code to the Replicators, and thereby return them to their ancient war with the Wraith: but it risks exposing her to Oberoth (David Ogden Stiers). Meanwhile, Colonel Samantha Carter and the Apollo search for the lost city.

When Ronon encounters some old companions, they tell how they survived when Sateda fell. Samantha Carter, the new head of the Expedition, considers them a security risk and is reluctant to allow them access to Atlantis, forcing Ronon to choose whether to leave with his former allies. Unbeknown to him, they harbor a dark secret as to how they really survived.

After coming across a crystalline species on M3X-387, similar to one which Jack O'Neill encountered in the SG-1 season 1 episode Cold Lazarus,[4] Sheppard inadvertently carries it back to Atlantis after contact with it. The being can travel through electrical conductors, and can enter the minds of humans through touch, where it causes nightmares - which eventually kill Dr Kate Heightmeyer.

Sheppard is captured by a race of humans who have lived for generations in space to avoid any Wraith contact, and who have heard rumors of a powerful enemy against the Wraith: the Atlantis Expedition. Now they intend to use Sheppard to activate an Ancient warship.

A deadly disease courses through Atlantis, causing the entire expedition to lose their memory. Teyla and Ronon have retained their memories and must convince everyone to work together to find a cure, before all their memories are gone forever.

While on an offworld trip to New Athos, Teyla and Dr Jennifer Keller discover that the Athosian settlement has been abandoned in the wake of the arrival of the Bola Kai, primitive warriors who don't want them to get off the planet alive. This also raises a larger question: what has become of the Athosians?

Searching for the missing Athosians, the team finds Davos (Martin Jarvis), a man of a primitive civilization called the Vedeenans. Davos can see into the future and bears news about an attack on Atlantis. Meanwhile, the Replicators introduce a new tactic in their war with the Wraith: the extermination of their food supply! As human worlds come under attack, the Wraith warrior captured by Kolya a year ago, nicknamed 'Todd', proposes an alliance with Atlantis to shut down the Replicators attack code.

McKay's sister, Jeannie Miller, is kidnapped on Earth by industrialist Henry Wallace, who believes McKay can save his dying child using the Replicators’ alien nanotechnology. McKay goes to Jeannie's rescue, but is inadvertently captured. To save their own lives, the two of them must prevent Wallace's daughter's death -at the risk of setting the Replicator Nanites loose on Earth.

When a mysterious drone collides with Atlantis, the team wonder whether the Replicators may have found the city and if Davos's prediction of its destruction will come true. Events quickly suggest that the Replicators are already among them; yet things become even stranger when Elizabeth Weir reappears.

The Atlantis team hope to eliminate the Replicators once and for all, by using their contacts with the Wraith known as Todd to recruit a fleet of Hive ships to fight alongside the Daedalus and the Apollo. Unfortunately, not many Wraith ships flock to the cause, and the Expedition set off a chain of events which they are not able to contain.

The Atlantis team successfully salvage a damaged Hive ship following the battle with the Replicators, and in the process retrieve some critical information that may help in their never-ending war against the Wraith.

An imposed lockdown of Atlantis, caused by a medical alert, traps key personnel in various parts of the city alongside people they never expected, threatening some relationships within the expedition and allowing others to bloom.

Offworld on a familiar planet, Sheppard and McKay agree to escort a young princess, Harmony, to some ruins where she can assume the title of Queen. On this simple and routine mission, they find that a Genii contingent is hunting Harmony down, on the orders of her own sister, who wishes to succeed to the title in her place.

When Sheppard's father dies, he and Ronon return to Earth to attend the funeral; but their plans are interrupted when they discover that a human-form Replicator is on the loose in San Francisco. Upon closer investigation, they learn it was created illegally by a scientist on Earth, who has programmed it to evade re-capture.

While offworld, Dr McKay, Dr Keller, and Col Carter become locked in an underground cavern, with no apparent means of escape. To while away the long hours, the three try to make the best of it, and attempt to get to know each other a little bit better.

At a request from Col Carter, Teal'c makes a journey to Atlantis to help out Ronon, who is up for review by the I.O.A.; but tensions rise when the two warriors learn that a group of Wraith have infiltrated the Midway station - and Earth!

As a mysterious new illness begins to spread throughout the Pegasus Galaxy, Teyla is convinced that the father of her child is trying to communicate with her through telepathic visions concerning it. But when Dr Keller discovers it to be a re-engineered form of the Hoffan virus (Poisoning the Well), which renders surviving humans poisonous to the Wraith, the team suspect that Michael is seeking revenge again.

The team are stunned when Dr Carson Beckett turns up alive. But when Teyla is captured by Michael they must perform a daring rescue mission using the information Carson Becket has obtained, which could play right into Michael's hands. Teyla, meanwhile, learns some important information about her people: and about Michael's intentions for her unborn child.

When Sheppard returns from searching for Teyla, he finds that Atlantis has been abandoned. The city is surrounded by a vast wasteland of sand dunes. As the last man in the city, he must uncover the reason for this strange turn of events, aided by information left behind by Dr McKay. Can he locate his missing team in time to prevent Michael from killing them all?

Carter launches a rescue operation for the victims of a huge off-world explosion; but the rescue party must combat Michael and his army, who also wish to recover the survivors. Michael is ultimately defeated and Teyla, who gives birth to a son, is rescued. (last appearance of Lt. Aiden Ford, Rainbow Sun Francks)

The clone of Dr. Carson Beckett is removed from stasis to receive a possible cure, and in turn is the only one who possibly can find a cure for a serious medical problem before it is too late for one of his closest friends. Dr. Keller is being used to grow a Wraith ship which takes over a section of Atlantis.

Ronon is reunited with Tyre, a former Satedan warrior turned Wraith worshiper (from season 4's Reunion). Having apparently turned on his new masters and broken free of their brainwashing, Tyre hopes to rebuild his destroyed relationship with Ronon and Atlantis. But things go badly when Ronon is kidnapped by a Wraith who tortures him, and a non-lucid Tyre may be the only person who can save Ronon before the Wraith brainwash him. After going through withdrawal from the Wraith enzyme, Tyre leads the team to the lab where Ronon is, but turns on them to get another fix after Ronon is revealed to be brainwashed. The Wraith tries to torture Sheppard, but Tyre reveals that he was faking his return to the Wraith and battles Ronon while Sheppard battles the Wraith. The rest of the team, having earlier been freed by Tyre, stun Ronon and Tyre sacrifices himself to blow up the lab and let the others escape. On Atlantis, the team manage to break Ronon's brainwashing and he mourns his old friend.

The Daedalus appears in orbit, abandoned, when the team know it is currently on its way to Earth. Investigating, they discover that this is not the real Daedalus. It is jumping between different realities, powered by a so-called alternate reality drive. Now the team is up against the clock: they must figure out a way to get back to their own reality before the drive burns out. They must also overcome the daunting discovery that another version of themselves explored the ship and died trying to do the same.

Dr. Elizabeth Weir (now played by Michelle Morgan) returns to Atlantis in the form of a digitally ascended being, who hopes to use Atlantis to construct human bodies for her consciousness and for those of eight other Replicators who likewise hope to Ascend. Weir convinces the team to allow the other Replicators to rebuild their bodies after she summons them once she rebuilds her own as FRAN, the Replicator McKay had previously created in order for them to build themselves human bodies to live in. However, one of the Replicators, Koracen doesn't like it and escapes the lab in order to remain a Replicator and seek Ascension. When he tries to kill Sheppard, Weir destroys him and realizing that she and the other Replicators are too much of a threat, sacrifices herself to trick the other Replicators through a Spacegate where they are frozen forever by the cold of space and deactivated.

After a mission to M44-5YN, a planet undergoing global warming, Rodney McKay begins suffering from the Pegasus Galaxy's equivalent of Alzheimer's disease. In the hope of saving him, the team bring him to Talus, a planet once inhabited by the Ancients, to a shrine which overcomes the symptoms of the disease for one day.

Sheppard and Beckett join Major Anne Teldy’s team on a planet with one of Michael’s research facilities for the early versions of his human-iratus hybrids concealed inside a cave system. The team battles the hybrids and kills them. And Beckett, who helped out, leaves Atlantis for good to travel the galaxy and help the people out there. Paul McGillion guest stars as Carson Beckett and Nicole de Boer guest stars as Dr. Alison Porter.

Teyla is posing as Todd's (Christopher Heyerdahl) Wraith Queen, giving him the authority to enter talks with another hive and its Queen in order to get the Wraith to use a new gene therapy to eliminate their need to feed. It's not too long before suspicion is cast upon them after Todd kills the other Queen and they must work together to maintain their plot. Teyla ends up taking the Queen's hive into battle with a rival hive in order to kill as many Wraith as possible. Teyla's hive is nearly destroyed, but Sheppard and the rest of the team arrive in a Puddle Jumper and severely damage the other hive, allowing Teyla's hive to destroy it. The team is captured and Teyla's interactions with them cause the suspicious Wraith to try to kill her, but Todd saves her and kills the Wraith. Teyla leaves Todd in charge of the hive and its alliance and returns to Atlantis where she is returned to normal.

The team comes to the aid of a village under Wraith threat, but Ronon and McKay must rescue one of their own when Dr. Keller is kidnapped by another Runner, like Ronon, named Kiryk, who has brought Wraith hunters to the planet. Ronon is forced to act as a Runner so he can save Dr. Keller from Kiryk. It is eventually revealed that Keller was kidnapped because he needed her help to treat an injured little girl traveling with him and he only kidnapped her out of desperation as he couldn't risk her refusing to help. Keller treats the girl and having earned Kiryk's trust, disables his tracking device so he can be free like Ronon before they hook up with Ronon and McKay. The group defeats a Wraith attack, but find the Stargate guarded by a group of Wraith and two Darts. Kiryk lures the Wraith through the Stargate to another planet and his fate is unknown, but his sacrifice allows the group to return to Atlantis where the little girl recovers and is adopted by a family on the planet where Keller was kidnapped as her own planet was destroyed.

Daniel Jackson returns to Atlantis to do research on the Lantean scientist Janus. But after finding one of Janus's secret labs, McKay and Dr. Jackson disappear after an alien ship appears in Atlantis and First Contact goes less than well. Woolsey goes aboard the Daedalus with Ronon and Keller and meets with Todd to discuss Dr. Jennifer Keller's gene therapy. The aliens force McKay and Jackson to activate a device that will destroy Wraith ships when they enter hyperspace, but with the side-effect that Stargates will explode when they are activated. Todd believes he has been betrayed and hijacks the Daedalus while Atlantis manages to track down McKay and Jackson but has the Stargate explode when trying to reach the Daedalus to reach the planet as it has no Stargate.

Sheppard and Zelenka survive the Stargate explosion, but the city is severely damaged. Todd forces Sheppard to give up the location of the Attero Device and heads there in the Daedalus, but is disabled by Ronon and Keller who escape Wraith capture. Keller is captured and the Wraith fix the hyperdrive and continue their journey, but their delay allows Sheppard, in a Travelers ship sent by Larrin to reach the planet first and engage the aliens who are revealed to be rogue Asgard. Todd and the Wraith flee the Daedalus after sending it on a collision course, but Sheppard saves the ship. McKay and Jackson escape and disable the device, but Jackson is badly injured before the Daedalus rescues them. Sheppard's ship defeats the Asgard, except one ship that flees and then destroys the facility where the Attero Device is to prevent it from ever being used again.

Sheppard and his team meet a man and a woman named Sefaris and Novo, two of a group of survivors from the planet Balara who survived the Hoffan plague and are now living with the people Dr. Beckett is helping. However, the Balarans face betrayal by their host village when the Wraith come hunting for them. The Wraith capture Beckett and McKay and force them to work on a system to detect survivors of the Hoffan plague, but it allows Beckett to determine he has the drug too and he uses it to kill the Commander and escape. The two disable the hive ship's weapons and escape, allowing Sheppard and the others to defeat the Wraith on the planet and escape with the villiagers and the survivors through the Stargate to Atlantis where the people are relocated.

The Atlantis expedition is put on trial for the crimes against the Pegasus Galaxy by a group of human civilizations that have formed 'The Coalition'. And one Latiran dignitary on the Coalition maybe working for the Genii. Richard Woolsey eventually comes to the Coalition and defends the Atlantis team, despite the Latiran dignitary and a woman who blames them for the destruction of her homeworld by the Asurans. Woolsey eventually manages to convince the one unbiased judge that they are innocent while convincing the one working for the Genii that Atlantis would be better as the military power of the Coalition causing them to get found not guilty despite the woman's guilty vote. This episode is a clipshow.

In search for Teyla's baby, Michael and his hybrids infiltrate Atlantis. While the hybrids take control of the city's systems one by one, it is up to Sheppard's and Lorne's teams to retake the city. But first McKay has to disable a seemingly impenetrable stun energy field set up by Michael. Teyla escapes with her son thanks to Woolsey and Ronon and McKay, Sheppard, and Zelenka manage to defeat Michael's plan, forcing him to flee when Sheppard and a strike team kill his remaining hybrids. Michael is finally defeated by Sheppard and Teyla in a hand to hand fight and Teyla finally kills Michael by throwing him from the top of Atlantis' Control Tower.

John Sheppard has been abducted. After freeing himself from his bonds, he soon discovers who it is who tied him up: Acastus Kolya (Robert Davi). In Atlantis, Woolsey, McKay, and the rest of the team are about to make a shocking discovery about an ancient race called Sakari, a silicon-based lifeform, which uses severe hallucinations into manipulating them into doing the right thing when a Sakari seed carrier is found in the ocean. Xiao Shen, an IOA dignitary, comes aboard to judge Woolsey's ability to be a capable commander and is planning on using this situation so she can get control of Atlantis herself. Eventually its revealed that both Kolya and a woman Woolsey was attracted to are projections of the Sakkari AI trying to distract Sheppard and evaluate Woolsey. The AI wants Woolsey's help to save its race from extinction by transporting it to its target world after it had crashed on Atlantis' home world thousands of years ago. It was trying to distract Sheppard as he was the greatest threat to it, but it never meant him any harm. Woolsey decides to help it even though it could cost him his job and has the Apollo transport it where it needs to go. As a final thanks, the AI tricks the dignitary and saves Woolsey's job.

Rodney McKay is invited to a landmark scientific presentation by an old rival from his school days and takes Keller with him. The device appears to be a solution to global warming, but then everything goes awry. The plan, using a matter bridge to transfer heat to an alternate reality based off the work McKay and Jeannie did in McKay and Mrs. Miller backfires when it won't shut off. Eventually the bridge is shut down and after McKay saves Keller's life she admits she loves him and they start a relationship. Guest Stars include Dave Foley, playing Malcolm Tunney, with Bill Nye and Neil deGrasse Tyson playing themselves.

The team investigates mysterious happenings on board a Wraith Hive, where Todd and his crew are suffering from a disease, just to find that since Wraith ships are organic, the ship has the disease as well. It's revealed they got this disease when they tried Keller's gene therapy which did work, but left them with a weakened immune system. Todd offers a possible solution: allow them to be fed on by an iratus bug queen but Sheppard refuses. At the same time the team has to deal with feral Wraith warriors and the ship's deteroiating condition. Eventually the ship splits in half, killing all but the team and Todd, but the front half falls into the planet's atmosphere. Todd manages to land it in the ocean and everyone is rescued by Atlantis before the ship sinks. Keeping a deal he made with Todd and believing Todd could be a powerful ally, Sheppard sends Todd through the Stargate to seek his cure.

Dr. Jennifer Keller is diagnosed with a psychological ailment. However, little does the Atlantis expedition realize that she has been exposed to body-switching technology, similar to the one that SG-1 found in the SG-1 episode Avalon that does not require the subjects to be in close proximity. Meanwhile Keller's consciousness faces a desperate struggle for survival inside the body of a wanted fugitive woman named Neeva. Eventually the team finds the device and Ronon destroys it just as Keller is about to be killed by Neeva's associate. Neeva is then presumably killed by her former associate, but both disappear so her fate is unknown.

In an alternate reality, Detective John Sheppard and FBI Agent Richard Woolsey find themselves in the midst of a CSI-like murder case involving several killings apparently of Wraith origin in Las Vegas, Nevada. It's eventually revealed that this Wraith is the only survivor of a hive ship that attacked Earth and was destroyed. The Wraith plans to send a transmission to the other Wraith to lead them to Earth, but Sheppard finds him and enters a gunfight that leaves Sheppard mortally wounded. As the Wraith is about to kill him, two A-10 Thunderbolt IIs sent by Woolsey - whom Sheppard alerted earlier - arrive. The Wraith quickly activates his transmitter before the fighters destroy it and him. The transmission never reaches Pegasus, thus saving the alternate Earth, but is sent through to other realities where it will reach Pegasus. As the episode ends, Sheppard crawls away from the wreckage and presumably dies, but seems at peace. This episode was filmed in Las Vegas, with filming for the season ending there, but it aired as the 19th episode.[5] During the episode, the songs The Beautiful People by Marilyn Manson, Sympathy for the Devil by The Rolling Stones and Solitary Man by Johnny Cash are played. The whole episode is filmed in the style of CSI.

Todd informs Atlantis that a group of Wraith have in their possession several ZPMs which they plan to use to power a new super Wraith Hive. He also advises Woolsey that they should immediately destroy it. But when the team reaches the hive, it does significant damage to the Daedalus and jumps into hyperspace. The team then finds out that the ship has received the signal sent from alternate Earth in Vegas and is heading to Earth. The hive shrugs off all efforts to destroy it, including an attack by Atlantis itself, but at the last minute, Sheppard destroys the ship with a nuclear weapon and saves Earth. Atlantis is forced to land on Earth due to lack of power.