The SGC are loaning their Goa'uld Mothership to their good friends and allies, the Tok'ra, so they will be able to move to a planet that is not on the gate system. However, Tanith is caught out and tells Apophis where the Tok'ra are.

SG-1 returns to a planet they helped free from Goa'uld enslavement, but its people are not happy to see them. Instead they are angry that the Goa'uld came back when SG-1 told them they wouldn't. Complicating matters, SG-1 doesn't remember their previous visit.

The SGC is infected by an alien probe that downloads itself into the base computers, accessing sensitive data on the SGC and its personnel.

During a visit to the Air Force Academy, Carter makes the acquaintance of Jennifer Hailey, a promising young cadet with great potential, but also a rebellious streak. Carter decides to show her what she can look forward to if she stays the course - by bringing her through the Stargate.

A member of another SG team, returning from an alien planet, commits suicide. The rest of his team begins to go into comas, and Daniel, who also visited the planet, attempts suicide. SG-1 must determine the cause before it is too late.

Daniel recovers Apophis's son, the Harcesis. He has the memories of all the Goa'uld, which the SGC wants to obtain so that they can defeat their enemies. Daniel is given all the knowledge, but soon begins to use it in a tyrannical fashion.

Nine years in the future, the Goa'uld have been defeated thanks to an alliance with an advanced alien race. However, Carter finds out that most of the human race has secretly been rendered sterile by Earth's new allies.

When General Hammond announces he is stepping down as head of the SGC, O'Neill suspects that there is more to his decision than he is letting on.

While visiting Chulak to gather support for a Jaffa rebellion, Teal'c is captured by the Goa'uld. The rest of SG-1, unaware of his fate, are dispatched by the Tok'ra to thwart a burgeoning alliance between Apophis and Heru-ur.

When Daniel Jackson's old archeology professor, Dr. Jordan, dies in a mysterious lab explosion, Daniel must return to visit his old academic stomping grounds.

A test of the X-301, an experimental aircraft adapted from two Goa'uld death gliders, goes awry sending O'Neill and Teal'c hurtling out of Earth's orbit.

Martin Lloyd, a conspiracy nutjob, calls up the SGC but has accurate knowledge of the Stargate. Martin claims to own a spaceship and is dismissed as a crackpot, but a series of incidents suggests that there may be more to his claims.

SG-1 are brainwashed and given memories of new lives and put to work as mining slaves on an alien world. While Hammond tries to find out if they're still alive, the SG-1 must struggle with their returning memories and plot their escape.

SG-1 helps transfer the residents of a Goa'uld slave planet to a new world, but soon find the planet is the target of a terraforming effort that will wipe out its new inhabitants.

An archaeological team makes an amazing discovery - a planet holding primordial Goa'uld symbiotes. But the planet also is home to the Unas, the first race that acted as a host to the symbiote, and the team and SG-1 are soon in danger from the symbiotes.

The Russians ask for assistance when they reveal they have the second Stargate, but it has become locked onto an alien water planet, not only preventing the SGC's Gate from functioning but endangering the Russian base.

When an alien scientist activates a device that the Ancients created for time alterations, Jack and Teal'c get caught in a time loop.

During a meeting of the Tok'ra High Council, one of the SGC soldiers goes berserk and attacks them before taking his own life. It soon becomes clear that the Goa'uld have a new weapon - a mind control technique that can turn anyone into a preprogrammed assassin. SGC soon realizes that Jack and Sam may be the next programmed assassins.

Teal'c's former love Shan'auc travels to Earth to ask for assistance - she has a way to tap into the memories of her symbiote and convince it that the Goa'uld are evil.

The Tok'ra ask the SG-1 to test some mysterious alien armbands, and they prove to confer vast super strength and speed on its wearers. SG-1 put their new-found "powers" to good use, but it soon becomes clear the armbands have a time limit that endanger the team in the midst of a critical mission.

An alien race, the Eurondans, contact the SGC and ask for help. SG-1 delivers humanitarian aid to the aliens, who have been devastated by war by a hostile power, but must make a decision when Alar, the Eurondan's representative, asks for military assistance against their enemy.

While Carter helps the Asgard fight the replicators galaxies away, Teal'c, Daniel, and O'Neill must contain them on Earth.