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.

Jackson discovers that his wife has returned to Abydos, and is nine months pregnant with the son of Apophis. O'Neill must keep the secret of the Stargate program from being uncovered.

While searching for the Lost City of the Ancients on a distant planet, SG-1 is stunned to find Daniel Jackson alive and in human form but stripped of his memory. O'Neill convinces Daniel to return with them to the SGC, where he is reinstated for a daring mission to destroy Anubis' powerful new super-weapon!