SG-1 discovers an ancient artifact and brings it back to the SGC. Ariving at the SGC, it becomes active, pins O'Neill to the gate room wall, and unleashes a virus into him.

SG-1 travels to a planet whose people are allies of the Asgard.

Stargate Command opens a wormhole to a planet with a black hole in orbit.

Following on a Tok'ra tip, SG-1 goes to a planet where they find the hated Apophis, nearly dying and under attack by death-gliders. They get back with him, realizing he was tortured by a rival system-lord with lasting harm. Apophis demands sanctuary, provided Dr. Fraiser can save his life, at least on account of the human host, but without a sarcophagus the prognosis for his symbiont is lousy; he offers all his Goa'uld knowledge in exchange for a new host, i.e. his life, revealing he was defeated by the terrible Sokar, once supreme system lord till an alliance lead by Ra and Apophis unseated him. The confrontation with Daniel, on account of Amaunet/Sha're and their son Klorel, and with former prime Teal'c, is bitter for all three. The Tok'ra send Martouf to warn the Tau'ri must hand over Apophis, but their warning is ignored- until Sokar proves he can bombard the iris with accelerated particles and ultimately cut through it, so the White House orders his extradition, but before they can he dies, unlike his host, an Ancient Egyptian temple scribe of Amun.

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.

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.