When powerful aliens come through Earth's Stargate, Colonel Jack O'Neill returns to Abydos to retrieve Daniel Jackson, who has discovered that the alien transit system includes much more than the two planets.

Colonel O'Neill, leading the new SG-1, track Apophis back to the planet Chulak to rescue Sha're and Skaara, and befriend one of Apophis' Jaffa guards.

Daniel is taken captive by an alien with a hidden agenda, while SG-1 is made to believe he is dead.

When Daniel goes insane, SG-1 must deal with the legacy of Machello's anti-Goa'uld technology.

His mind altered by Apophis, Teal'c must undergo a ritual that takes him to the edge of death itself, in order for him to rediscover who he is.