The Stargate base is put in deadly peril when it is contaminated with a dangerous infection which causes its victims to become mindlessly animalistic brutes.

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.

O'Neill, Carter and Jackson are trapped on Hathor's planet. Teal'c and Hammond go to Chulak to forge a rescue plan and recover the team.

Col. O'Neill is dismissed from the SGC for stealing alien technology, and is subsequently approached to participate in an even more covert Stargate operation.

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?