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.

SG-1 is put on trial and exiled to a prison world, where a woman maintains a strange control over her fellow prisoners.