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. Elizabeth Weir, 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.

General O'Neill is still in the early days of commanding the SGC and faces a major problem when newly arrived Russian Col. Alexi Vaselov collapses in his quarters. Dr. Brightman's belief that Vaselof may be contagious seems correct when Daniel, who was with the Russian when he collapsed, apparently goes mad and tries to leave the base through the gate. O'Neill locks down the SGC but the problem isn't contagion: the essence of Anubis is alive and well and seeking a new host.

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 is adapting a virtual reality chair for use as a training device. Teal'c thinks its current scenario is all too easy and agrees to work with them to make it more realistic. He enters the game scenario and is quickly "killed" at which point the chair shocks him. Lee says it must be part of its basic construct. As the scenario resets - it's an invasion of SGC by Goa'uld - Teal'c is repeatedly killed and shocked putting him in danger. The computer program is set up to learn after each scenario and the challenge for Teal'c increases at every turn. Daniel volunteers to enter the game as well to see if together they can find a way out.

Having obtained permission to live off the base, Teal'c rents an apartment, telling neighbors that he has recently arrived from Mozambique. He's under orders to keep a low profile but can't seem to help himself when it comes to helping his neighbors. He helps one who is about to be assaulted by three thugs, but it's his next-door neighbor who seems to need assistance. Krista is having problems with her boyfriend, Doug. Teal'c soon realizes that Doug is beating her and warns him that should he hurt her, Teal'c will kill him. It all becomes very difficult when Doug is found dead in Krista's apartment. Daniel Jackson soon after receives an offer - translate a Goa'uld text, and he will get ironclad evidence that Teal'c is innocent. Meanwhile, Carter is shocked when her boyfriend Pete Shanahan tells he asked for a transfer to the local police department and asks her to marry him.

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.

After a long absence, Jacob Carter returns to the SGC to tell Jack that the galaxy is under threat of takeover by the Replicators. The Goa'uld are under attack from the Replicators and are quickly being eliminated. Ba'al's armies are being destroyed and he arrives at SGC to suggest they work together to defeat their common enemy. Carter's doppelganger, RepliCarter, is leading the attack and she has kidnapped Daniel Jackson in the hope of learning of any weapons the Ancients may have created that could defeat them. Jackson gets help from an unexpected source - the Ancient, Oma Desala - or so he thinks.

Sam and Jacob are on the planet Dakara trying to configure the Ancient's device to destroy the Replicators once and for all, helped partly by Ba'al and Daniel, who succeeds in freezing the Replicators by manipulating Carter's duplicate.

Daniel finds himself in a strange time and place - a diner where Oma is working as a waitress. She gives him a clear choice - he can choose to die or to ascend but if it's the latter, he will not be able to help his friends fight Anubis, who has yet to be disposed of. He strikes up a conversation with another patron, Jim, who has his own take on the situation. Meanwhile, Sam decides the time has come for her fiancé to meet her father, Jacob. Jacob is not well, however, something he has kept from Sam for several weeks. After Pete surprises her - he thinks he's found the perfect house for them - Sam realizes she has to come to grips with her feelings for someone else. Teal'c and Master Bra'tac have information that Anubis may be gathering what remains of his forces for an attack on Dakara.

With the threats of both the Replicators and the Goa'uld greatly diminished and the sister ship to the Prometheus, the Daedalus, 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's time machine to take it from Ra at Giza in 3000 BC.

SG-1 has changed the course of history and made the 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 Chulak to find Teal'c.