Carter and Teal'c go in search of the Asgard to try and save Colonel O'Neill, but discover that the Asgard's enemy has returned with a vengeance. The System Lords seek an alliance with Earth against a common enemy.
While the Goa'uld threaten to attack Earth, SG-1 and the Asgard make a last, desperate stand against the Replicators, which have captured Major Carter and invaded the last outpost of the Asgard civilization.
An outbreak of disease is in fact the effect of possession by the ethereal remains of Anubis. Anubis escapes the SGC through the Stargate, though Carter alters his destination to a frozen, barren planet.
When SG-1 goes missing, Ba'al demands a ransom. After giving the SGC a booby-trapped ZPM, Camulus makes a deal to return to Ba'al on an assassination mission.
Tegalus is a world divided between two nations engaged in a cold war: the Rand Protectorate and the Caledonian Federation, both of which possess a large arsenal of ballistic missiles. When the SGC sends a MALP to Tegalus, religious fanatics who still worship the Goa'uld start a short-lived coup d'etat in the Rand Protectorate triggering a war.
Teal'c is trapped in a virtual reality training machine that delivers electrical shocks when he fails his objectives. Daniel enters the game in an attempt to save Teal'c from cardiac arrest and together they fight against the increasing difficulty of the game.
Teal'c moves into an off-base apartment, where he becomes involved with his neighbor, Krista, who has an abusive boyfriend. Teal'c is accused of murdering the boyfriend and Daniel disappears while trying to prove Teal'c is innocent.
Alec Colson, the powerful leader of aerospace and biotech conglomerates, holds a press conference to announce that aliens exist, that they have already attacked Earth once, and that several governments are aware of this fact. Colson gives the governments involved 24 hours to tell the truth. When the time expires, he shows a living Asgard alien to the media.
Rya'c plans to marry a woman of the Hak'tyl, which makes Teal'c angry. Ishta brings the Hak'tyl to the SGC because they believe that their location has been compromised. Carter attempts to find a suitable planet for them. The Goa'uld Moloc captures Ishta on a planet named Goronak. Ultimately Moloc is killed by missiles from the SGC, but his forces are taken over by Ba'al.
Having recently acquired the Tok'ra symbiote poison, the Trust steal the Stargate and start using it to launch symbiote-poison attacks against Goa'uld-occupied planets, killing thousands of Jaffa in the process. Cut off from Earth, Teal'c arranges to be captured by undercover Tok'ra Zarin on P3S-114 to find out if the Tok'ra are behind the attacks. The Trust captures Carter and brings her aboard the Alkesh where the Stargate is, but she's rescued by Daniel and Teal'c who beam aboard and use the
RepliCarter informs the SGC that Fifth has made all Replicators immune to O'Neill's disruptor, and promises to help them modify the weapon. In fact, her presence was needed to develop the immunity. She destroys Fifth and escapes to lead the replicators.
The crew of the Prometheus are incapacitated and removed, except Daniel, when it is hijacked by Vala, a pirate. Vala wishes to trade the ship for Naqahdah, but Daniel succeeds in retaking control of the ship and with the help of the crew in an Alkesh, fends off a Goa'uld attack that leaves Prometheus too badly damaged to finish the mission. Vala ultimately escapes in the end.
SG-1 finds that Harry Maybourne has become king on the planet where he took forced retirement. The planet is now under a Goa'uld threat, but Maybourne has found writings by a time-traveling Ancient that prophecy SG-1 will defeat the Goa'uld Ares. Ares sends Jaffa to the planet and comes in his mothership, but his forces are defeated by Daniel and Teal'c and his mothership is destroyed by O'Neill with the time traveling Puddle Jumper's weapons. Afterwards, Maybourne decides to remain on the plane
Russia and the United States reach DEFCON 1 because the Goa'uld may have compromised both governments via the Trust, which has been entirely assimilated. War is narrowly avoided when O'Neill convinces the Russian President of the truth and the Trust ship is destroyed by Prometheus, but the fate of Robert Kinsey is left unknown as he may or may not have been on the ship when it was destroyed.
An Indiana barber who carries the ATA Gene has his life ruined when, through an Ancient device, he begins to have visions of SG-1's missions. His life is given back to him when O'Neill informs his nearly-divorced wife of what had been going on.
The Replicators begin a systematic attack of the Goa'uld, forcing Baal to come to Earth for help. The Jaffa Resistance risk their entire movement in an attempt to retake a holy city in Baal's domain.
The fate of the galaxy hangs in the balance as Sam and Jacob search for the only weapon capable of stopping the Replicator onslaught. O'Neill leads a defense of the S.G.C., while Daniel squares off against Replicator Carter.
Daniel Jackson must choose death or powerless Ascension while Anubis plans to end all life in the galaxy using the Dakara Superweapon – until Oma Desala stops him. Jacob Carter and Selmak are in trouble. Daniel is returned to human form on Earth.
SG-1 travels back in time in a daring plan to steal a piece of Ancient technology from Ra, the powerful Goa'uld who ruled in ancient Egypt.
With the timeline changed by SG-1's actions in the distant past, an alternate version of SG-1 must use the newly-discovered time ship to set things right.