An alien similar to Ra appears out of the Stargate, killing five soldiers and kidnapping another, a year after the original Stargate mission. A new team is assembled, including some old members, and they go in search of the missing soldier in order to find out how Ra could still be alive. Meanwhile, the alien Gou'ald kidnap Sha're and Skaara, implanting them with symbiotes and making them Gou'ald hosts.

Colonel O'Neill, leading the new SG-1, track Apophis back to the planet Chulak to rescue Sha're and Skaara, and befriend one of Apophis' Jaffa guards.

Upon returning to the SGC from there first mission, SG-1 learns that Major Kawalsky, O'Neill's right-hand man, has become infected by a Goa'uld during their mission. As the SGC's doctors look for a way to remove the Goa'uld, Colonel Kennedy interrogates Teal's, who O'Neill wants to join SG-1. As time goes on and Kawalksy's mind is taken over more and more by the Goa'uld, doctors preform emergency surgery in a desperate attempt to save Kawlasky. But they prove to be too late as Kawlasky escapes and activates the base's self-destruct, leaving only Teal'c to stop him.

SG-1 arrives on a planet controlled by the Shavadai, decedents of Mongols, who view women as subservient and submissive. The presence of SG-1 Captain Samantha Carter causes an instant uproar. Carter is forced to adapt to the custom's, but is soon kidnapped by the chief's son who trades her in another village. As SG-1 tries to find her, Carter must survive in this society to bring about freedom for all women.

The Stargate base is put in deadly peril when it is contaminated with a dangerous infection which causes its victims to become mindlessly animalistic brutes.

The SG-1 team is sent after the SG-9 team that has failed to return. They find that SG-9's captain, having been treated like a god by planetary inhabitants, is drunk with power and is tyrannizing them. Can they overcome him?

On the planet Argos, Kynthia seduces Colonel O'Neil, which gives him an Argosian lifespan of only a 100 days. As his skin turns the color of death, will the SG-1 team succeed finding a cure?

When Jack is injured unintentionally by a crystal alien, the alien duplicates Jack's form and out of fear of retribution tries to heal Jack. He returns to Earth in place of Jack, while Jack is still unconscious on the planet, to find the one thing he feels will accomplish this; the one thing that cannot be found again. Meanwhile, the 'real' Jack has returned and is trying to convince SGC that he is who he says he is.

SG-1 goes to the planet Cimmeria in search of allies against the Goa'uld. Upon arrival, Jack 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. Daniel Jackson must destroy the device that could someday have saved his wife in order to free his friends.

Daniel Jackson discovers that the Stargate was activated in 1945 and a young professor went through, never to return. Together with his still living fiancée, the SG1 team discover the now aged professor, naked and trapped in a decaying fortress, containing the secrets of an Ancient alliance. Will they be able to rescue him and escape to earth in time?

It is time for Teal'c's son Rya'c to have his primtal. Can Teal'c stop his son from being implanted with a goa'uld and becoming a slave to Apophis?

O'Neill, Carter and Teal'c return through the Stargate shell-shocked and distressed to announce that Daniel Jackson was killed. But Jackson was captured by the last survivor of an aquatic race, who planted false memories in the other members of SG1. Can the team remember and return to rescue Daniel?

With the Stargate program in danger of being terminated, the team is under pressure to find technology. Visiting a planet where they believe there is a creature that possesses the secret of invisibility, they encounter Apophis and his guards. Both sides receiving mortal wounds, they are aided by the planet's inhabitants, the Nox, a gentle people with a very large secret.

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

SG1 travel to a planet where Teal'c is recognised as once having been head Jaffa to Apophis. He is arrested for the murder of a villager and put on trial for his life. Then other Jaffa attack the village. Will SG1 be able to save Teal'c and prove that he has changed allegiance?

SG-1 rescues a small girl who turns out to have had an inoperable Naquadah bomb put in her by Nirrti to destroy the SGC. Ultimately the girl is given to the care of Janet Fraiser, the SGC medic, after they discover that the bomb will dissolve if she is kept away from the Stargate.

On their first visit to a new planet, SG-1 finds it subject to totally destructive volcanic activity and saves ten natives, the Tollan, a far more technologically advanced society. Their leader Omoc isn't grateful, nor interested in such a primitive race as the earthlings or any of the 'even more primitive' planets which are prepared to host them. Only one Tollan, Narim, shows an active interest in life on earth, especially in captain Samantha Carter and the cat Schrodinger she gives him, explaining his planet was destroyed after the Tolan supplied an unlimited energy source to a primitive neighboring planet which abused it for a cataclysmic weapon. Meanwhile the White House authorized NID colonel Mayborn to take charge over the Tollan for military purposes, exactly Omoc's nightmare...

Upon arrival on planet OX3,989 the team are rendered unconscious. When they wake, they return to Earth, but soon find out that they are Androids. The team must return to the planet to find out what happened to their real bodies.

Following a Stargate technical defect, O'Neill and Carter are stranded next to a Stargate in a cave on an icy wasteland. O'Neill is severely wounded and both are freezing. Will the SGC find and rescue them in time?

While exploring an alien stargate complex on P3R-233, Daniel Jackson finds an alien artifact that appears to be a mirror and touches it, receiving a mild jolt. No thinking anything of it, Daniel goes to find the rest of SG-1 who appear to have left him behind. Traveling to Earth, Daniel finds himself in an alternate reality where O'Neill is the general in charge, Carter is a civilian scientist, Catherine Langford is the civilian head of the program, and where he never joined the program. What's worse is that the Goa'uld are invading Earth, killing 1.5 billion people. With Teal'c leading the Jaffa assault on Stargate Command, Daniel must escape through the stargate with information that might save his world from such grim fate or convince his counterparts in this alternate reality to help prevent a similar apocalypse in his own reality.

The Stargate team must justify the project's continuation when a doubtful senator, Head of the Congressional Military Appropriations Committee, comes to review the project's performance.

General Hammond has tried everything to get the senates decision to shut down his space program undone, but the president personally refuses to 'commit political suicide': the Stargate will be buried. Daniel's insistence the danger for earth as a whole outweighs everything convinces his military SG-1 colleagues to ignore the commander general's command and dial the address the goa'ald invasion started from in the parallel dimension he visited. They arrive not on a planet but a new, superior type of starship, already launched by hyper-drive. A 'video' proves it belongs to Apophis, who gives command aboard to his son Klorel, whose host is no other then the team's young Abydos friend Skaara, yet overpowering him seems their best move, while Sam installs explosives in the death glider deck with a 24 hours timer just in case, but Jaffa manage to liberate Klorel and the ship goes far faster then expected...