As the Goa'uld attack fleet approaches Earth, all four members of the SG-1 team are taken prisoner. They get help from an unexpected source when Bra'tac, Teal'c's mentor, reveals that he is on board. Apophis has delayed the attack until his son Klorel is revived, giving them some time to prepare. SG-1 has used all of the C4 on one of the two ships but must find a way to dispose of the second. Back at Stargate Command, Lt. Col. Bert Samuels arrives as a Pentagon liaison officer but also reveals a new weapon they have developed. General Hammond is dubious. They begin to transport humans to an Alpha site in order to ensure the continuation of mankind.

O'Neill and the team return to Cimmeria, the planet where they destroyed Thor's Hammer to help Teal'c escape. They find that the Goa'uld have invaded and many of the people are dead. Can they help to find Thor's weapons to fight off the invasion before they are all captured or killed?

While O'Neill and Carter head to Washington to be decorated by the President and find a security leak, Jackson and Teal'c go to Abydos (after they unbury their stargate) to see Sha're's father. They arrive to tell him that they have been unsuccessful in finding Sha're, only to discover that she is already on Abydos. But they find that she is pregnant by Apophis and the baby holds the secrets of the Goa'uld.

Colonel O'Neill awakens and is told by new staff everything in the SGC is different because he was just revived after 79 years of cryogenic hibernation, as sole survivor of a disastrous SG-1 mission on a Goa'uld-ruled planet. He accepts to undergo a 'high tech hypnosis' to retrieve information of use in the present war against them, which is going badly, involving earth's ten endangered colonies on other planets. However Major General Trofsky, the new base commander, and his female assistant tell Daniel and Sam, in different sections, that each of them is the sole survivor: it's all make-believe to probe their brains about the weaknesses of earth and the Alliance of the four races. Meanwhile, Teal'c awakes on earth, where it took Dr. Frasier months to save him from death; there was no trace of his teammates, and he resigns when General Hammond refuses permission to keep searching. O'Neill hears Goa'uld language, gets himself free and discovers he's on a fake SGC, frees Sam and Daniel, only to be stopped by the female Goa'uld system-lord Hathor, who employs both Horus and Serpent Jaffa and demands the humans' help against her rival system-lords.

Teal'c is on his home planet, Chulak, where there is rebellion among the Jaffa warriors. He is betrayed as a sacrilegious shol'va (traitor) by Rak'nor, son of a Jaffa friend of his father, and handed to Terok, the torturer of system lord Heru'ur. Ignorant of his fate, the other SG-1 members join Jacob in a risky attempt to take hold of a space mine using a Tok'ra ship piloted by Jacob. En route to Apophis' spaceship, the expedition finds out that Teal'c is being offered as a confidence-building present from Heru'ur to cement an alliance with Apophis against the other system lords, which would make the Goa'uld threat more dangerous than ever. They decide to save Teal'c, but their attempt fails. However, Teal'c's resistance to torture and clear conviction that Goa'uld are not gods finally convinces Rak'nor, who now bravely acts.