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.

SG-1 escapes through the Stargate before it is shut down, and learns that Daniel's alternate reality vision is true: Apophis is moving to attack Earth from above. The team must stop Apophis and his son, Klorel, who inhabits the body of their friend Skaara.