Despite the defeat of the Replicators, some survived the crash and managed to infest a Russian Foxtrot-class submarine to replicate a new army. Meanwhile, Thor returns to Earth and wants MajorSamantha Carter's assistance to defeat the Replicators from taking over Othala, by using "stupid ideas" as a means of stopping them.
The Eurondans, who have an ancestral history with the Tau'ri, contact Earth and request their assistance to win a generations-long war. However, the lack of intel about their "enemy" and their shady behavior arouses a lot of suspicion from Dr.Daniel Jackson.
Shan'auc, one of Teal'c's old flames and priestess of Chulak claims to have taught her symbiote to despise the Goa'uld. The Tok'ra seem convinced of this, but there is still a reasonable amount of doubt from the others.
On a routine mission to P4X-639, SG-1 meets an alien archeologist Malakai operating an Ancient device. Malakai has his own motives and causes a time loop, where only ColonelJack O'Neill and Teal'c notice. Furthermore, convincing the rest they are trapped in a time loop and that they have to return to the planet to stop it proves difficult when the same few hours from breakfast to the mission is repeated over and over again.
Stargate Command is unable to activate their Stargate. They soon discover that the Russians have their hands on one, after they recovered one from the wreckage of the crashed Biliskner. Another problem is that their Stargate is somehow still activated indefinitely.
Dr.Daniel Jackson is captured and taken prisoner by an Unas later to be known as Chaka on P3X-888. While he learns more about the Unas, the rest of SG-1 and other teams plan a rescue operation. However, Teal'c stops them, after he senses that one of the team members are taken host by a Goa'uld.
After Dr.Daniel Jackson learns that his old archaeology professor dies in an explosion, he soon suspects that it may not be an accident, and that one of the professor's colleagues are responsible for his death. Meanwhile, he finds out a shocking secret about the Ancient Egyptian artifacts they are studying.
SG-1 and Selmak receive solid intel that Apophis and Heru'ur are forming an alliance to rule the galaxy. They plan to use one of the mines from the Tobin system to attack the fleet. Furthermore, Teal'c is captured by his old friend Rak'nor, and is imprisoned onboard Heru'ur's vessel.
The Harcesis has been found on Abydos and taken to Earth by SG-1, where they tell him how to defeat the Goa'uld once and for all. However instead Shifu, the Harcesis shows Dr.Daniel Jackson a vision of what would happen if he gives him the plans to defeat the Goa'uld.
After an Lt.Dean Barber kills himself by the Stargate's unstable vortex and the rest of his team are mysteriously dying, SG-1 links the team's routine mission to P4X-347 to be responsible, as they find a highly beautiful, yet very addictive light.
CadetJennifer Hailey gets MajorSamantha Carter's attention after noticing her intelligence, which rivals Carter's. She decides to send her on a mission with an expedition team on M4C-862. There, the teams manage to anger a group of tiny flying orbs, which can literally pass through solid matter with fatal consequences for the teams.
SG-1 arrives on Juna, where they are captured by Cronus' forces, where Cronus himself doesn't take the reunion well. However, unknown to him, SG-1 is actually the robot copies from the real SG-1's encounter on Altair three years ago.