SG-1 gears up to save O'Neill and simultaneously confront the possibility of a truce with the Goa'uld. Meanwhile, the human replicators are intent on offering some vicious payback to the SG-1 team.
The arrival of a dangerous alien creature coincides with the arrival of a Russian Colonel to the SGC, but when the alien begins to control the minds and bodies of the crew members, O'Neill must order an immediate lockdown.
With his new appointment as general, O'Neill's resolve is tested when he must deal with several major conflicts, from squabling delegates, to Dr Lee's wildly-growing plant, to Ba'al's attempt to capture SG-1, making him quetion how well he will be able to handle his new responsibilities.
SG-1's appearance sparks a civil war, and Daniel Jackson must aid a battle-torn society.
Teal'c becomes trapped in a virtual-reality training scenario.
Teal'c decides to move into an apartment off the Stargate base, but soon finds himself suspected of kidnapping and murder, during which time Daniel sets out to prove his innocence. Meanwhile, Carter's boyfriend Pete proposes to her, giving her a big decision to make about their future together.
A wealthy industrialist attempts to reveal the secrets about existing alien life and blackmails the Earth's governments into spilling its secrets on the matter, leading Carter to try and convince him that the world's knowledge of alien life will do more harm than good.
Teal'c gets involved when his son Rya'c is about to marry a Jaffa Haktyl woman Teal'c feels is beneath Rya'c. Meanwhile, Carter helps the SGC shelter the Haktyl people, who are migrating to another planet to escape the Goa'uld.
The SG-1 team tries to determine the perpetrators behind a plot to steal the Stargate and the deaths of several Jaffa, deaths which may be a part of a larger Jaffa extinction plan.
The Replicator Carter requests that she be destroyed and reveals that the Fifth, who created her, has also instilled an immunity to disruption in all replicators. Carter's emotions run high as the team tries to figure out if her Replicator is being truthful or has a hidden agenda.
Daniel and General Hammond head for Atlantis on the Prometheus, but in the midst of salvaging a Goa'uld vessel en route, Daniel finds himself alone on the Prometheus and confronted by Kull warrior Vala, who claims the Prometheus can aid her in her quest to free her people from the Goa'uld.
The SG-1 team goes to save Colonel Maybourne, who was placed by the Tok'ra on a planet which is in now danger of attack, but finds that he has claimed rulership using the wisdom of the Ancients.
Robert Kinsey resurfaces and tells O'Neill that the Trust has plans to destroy the U.S. government. After Kinsey is tracked to Russia where he attempted to murder a Russian general, Daniel himself is captured and taken into custody.
A barber makes an unwelcome visit to O'Neill's home and claims that his life was ruined when he gained complete knowledge of the Stargate project through a mysterious stone. The event triggered an obsession which eventually helped ruin his business.
When a battle for control of the galaxy begins, the SG-1 team is forced to determine the extent of its loyalties.
As Carter and Jacob locate the weapon of the Ancients on the planet Dakara and try to figure out how it works, Teal'c and the Jaffa struggle to keep Ba'al and his ships from taking control of Dakara. Meanwhile, the Replicators take control of the SGC, while the Replicator Carter tries to drill Daniel for his wisdom of the Ancients.
The SG-1 team must look ahead to what the future has in store for them after working together for so long. Meanwhile, Daniel is faced with a critical life decision.
The SG-1 team uses the puddle jumper to head to ancient Egypt where they are on the hunt for a lost power source. When they are unable to get past the Jaffa to go back through the jumper, though, they soon find the future completely changed so that SGC has never come into creation and its members work in other fields, but a recovered video camera features the past Daniel telling the future about how to discover the stargates.
When the alternate SG-1 team tries to rescue Teal'c, Daniel is killed in the process, prompting O'Neill and Carter's alternates to seek out the first Daniel by going back to ancient Egypt, where they plan to snatch the first stargate and set the proper chronology in order.