When Teal'c makes Sam Carter realize how valuable the knowledge left by Tok'ra Jolinar in her brain and the chance for an alliance can be, they convince General Hammond to let SG-1 attempt a meeting. They arrive on a planet which is deserted on the surface, but are awaited by well-camouflaged, armed Tok'ra who bring them to tunnels which they create by means of a mysterious crystal, which can also undo them afterward. Both parties are quite suspicious, the team feels like captives, and indeed, the Tok'ra leader Yosuuf fears they cannot be released, at least until the whole site is moved. Meanwhile, the Tau'ri barely overcome their suspicion against the Tok'ra Goa'uld biology (with symbiote), when asked to volunteer themselves as 'hosts', and Carter learns Martouf (and his symbiote, Lantash) was Jolinar's lover, hence has a special connection with her.

The attempt to forge an alliance with the Tok'ra seems a miserable failure, as SG-1 is practically imprisoned as a security risk and considered virtually hostile because 'blending', by agreeing to host a symbiote, is a bridge too far for each of them. When SG-3 arrives and informs Sam about her terminally ill father General Jacob Carter's quickly worsening condition, she realizes the symbiote's healing powers, confirmed to apply to cancer, make hosting an offer to good to refuse for him. Garshaw allows Sam and Jack to return and convince both generals to allow the plan, which is achieved. Meanwhile, the Tok'ra must hastily evacuate, destroying tunnels behind them, because a large-scale attack by Apophis's troops is expected soon, while Jacob meets his potential symbiotic partner Selmak and his equally terminal predecessor to help him decide. Jack verifies his strong suspicion there is traitor among the Tok'ra who is communicating with the Goa'uld.

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.

Martouf leads a Tok'ra delegation with crushing news for Carter: her father Jacob/Selmak has been captured by Sokar and imprisoned on Netu, an Egyptian name for hell, on a moon of planet Delmal, where prisoners are sent to suffer eternal torture, and from where no one returns; only Jolinar has ever escaped. SG-1 mounts a rescue operation with Martouf, top-priority being any information Selmak can offer about Sokar's plan to subjugate the other system lords, an unprecedented threat for all humanoids in the galaxy. Teal'c must pilot a Goa'uld ship and keep it in orbit as landing is impossible except by small pod, but first Martouf taps into Jolinar's memory, which is partially blocked by some trauma beyond physical torture. Only when they're down and in the custody of Netu's lord Bynarr, does Sam realize he is the key, in a 'personal' way, but not voluntarily, as she had thought. Sokar learns of their presence from Bynarr and orders the team and craft destroyed, but this also means there must be a way out. Bynarr's prime, Na'onak, has, and is himself, a major surprise.

Now that Apophis has revealed himself, he promises the prisoners to overturn Sokar, which requires extracting an irresistibly valuable secret, to which end he drugs Sam with the truth serum 'blood of Sokar.' Apophis also implants a memory device in, and gives the drug to, Jack to torture him using the persona of his young son that died, and Daniel for the location of his Harsesis son. Martouf's love for Jolinar makes him betray that the Tok'ra are on planet Entac - a convincing lie, so Apophis's plan to earn Sokar's gratitude, and then kill him when rewarded with the lordship of Netu, is on a shaky basis. Teal'c must help the Tok'ra Aldwin prepare a nuclear weapon to explode the whole moon when his ship arrives as their last chance to eliminate Sokar, but he decides to rescue SG-1 instead, by flying in the path of the rings device on Sokar's ship when he arrives.

When an SG-team member tries to assassinate the Tok'ra leader, it is believed that some of the SGC have been converted into Za'tarc - programmed assassins. The Tok'ra Freya comes to the SGC with Martouf to try and test all SG-team members. But the Za'tarc detector suggests that O'Neill and Carter are actually Za'tarcs. Is this correct and is there another Za'tarc at the SGC?

SG-1 returns early from a mission only to realize that they and Gen. Landry aren't on the same page as far as the the mission they've just completed is concerned. The confusion is quickly resolved when the "real" SG-1 returns at the correct time. Dr. Lam examines them all and concludes that they are identical and thinks they might be clones. Sam however thinks they may have come from a parallel universe as the result of the black hole they created when they destroyed the Ori beachhead. As more SG-1 teams arrive from other alternate universes, one of them includes Dr. Fraiser and another includes the Tok'ra Martouf. It's left to Sam and Martouf to find a way to send them all home.