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.

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?

Teal'c is unhappy with his son's plans to marry. Ishta arrives bringing news that Hak'tyl may be compromised. Complications arise when O'Neill allows Hak'tyl to inhabit SGC until a new homeworld is found for them.

Vala is kidnapped by agents of the Trust who are trying to find an ancient treasure when an accident causes Vala to forget who she is.