In a last ditch effort, O'Neill activated an Ancient weapon in the Antarctic to defeat Anubis. With Jack still in stasis in the Ancient outpost buried in Antarctica, SG-1 tries to contact the Asgard. Meanwhile their new leader, Dr. tries to decide what to do about a request for peace talks from the Goa'uld System Lords.

The Asgard fleet has managed to destroy the Replicator ship, with Carter aboard, but cannot contain the debris. Talks break down with the System Lords, ending in a Ha'tak being dispatched to test Earth's new defensive capabilities. The Prometheus waits to engage the incoming enemy, but Thor arrives in the Daniel Jackson, with Teal'c aboard. They enlist the help of Daniel and Jack, still in stasis, to remove the threat of the replicators to the new Asgard homeworld.

Colonel Alexi Vaselov arrives at the SGC and soon becomes ill after talking with Jackson. When General O'Neill tries to have him put in quarantine, Daniel starts shooting, wounding two guards. Carter and base doctor Dr. Brightman determine that what made Vaselov ill and made Jackson start shooting wasn't a disease: it was Anubis, attempting to return to his empire to get a new body to possess. O'Neill places the SGC under lock down as SG-1 and the SGC attempt to force Anubis into some type of action. But the plan backfires and soon nobody can be trusted.

As the new head of the SGC, General O'Neill is beginning to feel the weight of his load, and he starts to have second thoughts about the whole idea, questioning his own competency.

The discovery of the Stargate creates a war between two nations on the planet Tegalus with Daniel in the middle of it.

Dr. Lee and his team have modified one of the virtual reality chairs last seen in "The Gamekeeper" to host a combat simulation for training Stargate personnel. After claiming the simulation isn't realistic, Teal'c agrees to help the scientists refine it. Inside, he faces steadily mounting hazards. Worse, his own ego prevents him from leaving until the last Goa'uld is destroyed. Each time he dies in the scenario, the chair shocks him. Teal'c must find a way past the barriers of his own mind to escape before the virtual deaths sum to real fatality.

Teal'c saves a young man from a vicious beating. This is just the latest in a series of "incidents" since he took an apartment off-base and the Air Force is not pleased. Daniel Jackson attempts to explain why and how to keep a low profile, but Teal'c cannot help getting involved with a young woman whose boyfriend abuses her. In doing so he inadvertently plays into the hands of a mysterious group with access to Stargate knowledge...

Owner and CEO of Colson Industries declares in a press conference that there is alien life and that he has proof. SGC fails in its attempts to keep him quiet on the battle over the Antarctic. However, they are greatly surprised when the proof he shows the media are not his satellite images, but a living Asgard.

Teal'c is unhappy with his son's plans to marry. Ishta arrives bringing news that Hak'tyl may be compromised. Complications arise when O'Neill allows Hak'tyl to inhabit SGC until a new homeworld is found for them.

When the Stargate gets beamed out of SGC in the middle of the night, Teal'c is stranded off-world. Dr. Jackson and Colonel Carter attempt to recover the gate.

The replicator Carter and the real Carter work together with the disruptor signal. The replicator has a different plan.

General Hammond returns to SGC to take Dr. Jackson with him on a trip to Atlantis onboard the Prometheus. In the middle of their trip, the Prometheus picks up a distress signal and Hammond decides to investigate. Things get sticky when a Kull Warrior takes control of the Prometheus, leaving Hammond and his crew, minus Daniel Jackson, behind in a damaged Alkesh.

SG-1 is sent to warn Harry Maybourne that the goa'uld System Lord Ares is coming to the planet where he was banished, and in the process they find what may be an Ancient time machine.

Ex-Vice President Kinsey comes to Jack informing him of the Trust's activities including what seems to be a plan for the Russians to reclaim the Stargate they lent to the United States. He decides to use Kinsey as their inside man with the Trust. Kinsey wears a wire for his meeting with the Trust to set up a meeting with a high-ranking Russian general. The plan goes south when the signals get jammed just as the Trust makes an astounding revelation to Kinsey and they beam out.

A man breaks into Jack's house and hold him at gunpoint claiming that Jack ruined his life. Seven years ago he came upon an Ancient artifact at a garage sale that allows him to see all of SG-1's missions.

When a goa'uld cargo ship is caught entering a neutral zone, it is learned that Carter is the pilot and is taken before the system lords. Then it is soon learned that she is the replicator version and has launched an all out war against the goa'uld. If the goa'uld can't stop the replicators, the replicators will overrun the galaxy in a matter of weeks. Can the people of the Milky Way find a way to stop them or will the galaxy fall to an enemy worse than the goa'uld.

The replicators are taking over the galaxy and are killing off the goa'uld. The replicators are becoming immune to any attack that is thrown at them. Then a way to destroy them is found: A weapon capable to destroy all life in the galaxy and dialing all the gates in the galaxy at once so that the replicators cannot adapt. The device can be altered to only destroy the replicators. That is why Baal and the real Carter join forces and the awesome battle for the galaxy begins.

Daniel encounters Oma in a strange celestial coffee shop for ascended beings, and their conversation may be the only way to save the galaxy from Anubus' plan to unleash the weapon on Dakara. Meanwhile Teal'c and Master Bra'tac lead Jaffa forces on a more traditional attack. Sam must come to terms with Selmak/Jacob growing ill and Pete pressuring her to commit to the relationship.

With the threats of both the Replicators and the Goa'uld greatly diminished and the sister ship to the Prometheus, the Deadalus, now under construction, SG-1 is anxious to get a ride on the new ship. However, the mood is somewhat darkened by a phone call informing Dr. Jackson of Catherine Langford's death. After the funeral, Catherine's niece gives Daniel "a few odds and ends" that her aunt wanted him to have. Upon delivery it is discovered that almost her entire collection was shipped to Daniel's lab. He finds in one of her books a possible location of a ZPM, but scans of the area showed that it was no longer there. Daniel proposes that they use the Ancient time machine to take it from Ra at Giza in 3000 BC.

SG-1 has changed the course of history and made SGC virtually non-existent. Doctors Carter and Jackson have helped Brigadier General Hammond to find the Antarctic Stargate, but are not being allowed to help any further. They help Jack to power up the time machine, and he gets Hammond to allow them on the mission to find Teal'c.