An old love of Teal'c approaches the SGC and the Tok'ra claiming that her Goa'uld symbiote has been convinced to defect with their help.

On Juna, SG-1 gets a hostile welcome from the local warriors' leader Darian, who seems incredulous they even dared to return. They loyally deliver Sam and Teal'c to Cronus and told them to bury the Stargate. Cronus orders Darian to decapitate Daniel by staff weapon- to find his head is robotic. Cronus's obvious astonishment makes Darian doubt his divinity. At the SGC, Harlan urge them to go on a mission. The master robot-creator tells SG-1 that the robot versions of them he created need to recharge after 48 hours. In order to prevent the Goa'uld gaining access to their duplicates' memories, SG-1 reluctantly go to Juna. Darian now joins them, but feels most of his people won't dare challenge Cronus. The two Teal'cs concentrate on revenging the original's father by attacking Cronus recklessly, while the Sams and Jacks deal with the military problems and overthrowing the Goa'uld rule.

To help Teal'c's mind clear again, SG-1 asks Bra'tac to help. Bra'tac removes Teal'c's Goa'uld and Teal'c is forced to remember certain memories of his past in order to get back to the real Teal'c in the end. SG-1 is glad to have him back.

A new leader has risen among the Free Jaffa, K'tano, former First Prime of Imhotep. SG-1, accompanied by Bra'tac, seeks an alliance between the Tau'ri and the large force he has amassed.

To fix a mistake caused by the fake SG team, the real SG-1 must enlist the help of two convicts. The threat of an approaching Goa'uld mothership stresses the repair of the Sentinel.

Master Bra'tac arrives with bad news: Teal'c's wife is deathly ill, and Teal'c leaves to be with her. Shortly thereafter, the gate is opened but nothing comes through. Then Carter discovers a very low power signal that is slowly building an overload powerful enough to destroy the Earth.

The Tok'ra are forced to evacuate their newly established base under attack from the Goa'uld. They flee to the SGC's Alpha site. Tensions rise between the allied factions, the Free Jaffa, Tau'ri, and Tok'ra. Jacob and Selmak feel the end of the Tok'ra is near and Sam finds a Naquadah generator has been sabotaged to function as a bomb. Jack suspects the recently arrived Tok'ra and attempts to weed out the traitor.

Senator Kinsey is shot in the chest at a public event, killing him just before his party's presidential nomination. Jack is arrested for the murder, and General Hammond assigns the rest of SG-1 to uncover the truth.

On a shakedown cruise of the Prometheus, the ship's hyperdrive regulator becomes irreparably damaged. A nearby planet was listed on the cartouche of addresses found on Abydos and thus may have a stargate. After a short jump towards the planet, the Naquadria reactor overloads and must be jettisoned. After the reactor explodes above the planet causing damage, the fate of SG-1 and the crew of the Prometheus is in the hands of a once Goa'uld-controlled world that they're off to a rough start with.

A teenage boy shows up at the SGC claiming to be Jack O'Neill. He recalls a dream in which an Asgard was studying him. They determine that they must find this Asgard to fix what has been done to Jack.

When an SG geological exploration mission runs into deadly conflict with an indigenous Unas clan, Daniel gets Chaka to help seek an accord with it.

The president has asked that a documentarian go to SGC to create a film about its operations. His arrival is unwelcome to most and he begins to clash with the base personnel. Nevertheless, he conducts his interviews with SG-1 and the scientists in the employ of SGC. Meanwhile, an off-world SG team finds the remains of an Ancient city.

The documentarian still a thorn in their side, SGC encounters an unforeseen predicament. With half of SG-13 off-world engaging enemy Jaffa, SG teams 1, 5, and 7 go in as backup. In the midst of heavy fire, O'Neill takes a staff blast to the chest. Many deaths from the encounter hit SGC hard and Senator Kinsey orders a full investigation into the matter.

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.

SG-1 is caught in the middle of a war after the Jaffa use a powerful weapon to kill 10,000 Ori followers.