When an incoming wormhole is established at the SGC, the iris is over-ridden and opened. A young boy appears and tells the SGC that they are in terrible danger from a group of terrorists. But these terrorists are invisible creatures and they are determined to wipe out all humans to prevent them being used as hosts to the Goa'uld.

The team discovers an early industrial world suffering from collective amnesia and has no elderly people.

A new leader has risen among the Free Jaffa, K'tano, former First Prime of Imhotep. SG-1, accompanied by Bra'tac, seeks an alliance between the Tau'ri and the large force he has amassed.

To fix a mistake caused by the fake SG team, the real SG-1 must enlist the help of two convicts. The threat of an approaching Goa'uld mothership stresses the repair of the Sentinel.

SG-1 is providing security for three scientists who are conducting research on a far-off planet. Goa'uld warlord Khonsu arranges to capture the SG-1 team and O'Neill tells Jay Felger, nominally the group's leader, to use the gate and head back to SGC. Felger is quite enamored with SG-1, admiring their exploits and daring-do. Rather than follow O'Neill's orders, Felger and another scientist, Simon Coombs, transport themselves up to the Goa'uld ship. What the scientists don't know is that SG-1's capture is a ruse to allow Khonsu, who is actually a Tok'ra, to pass on information. O'Neill is quite annoyed with the two scientists but their presence proves useful in the end.

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.

SG-1 is caught in the middle of a war after the Jaffa use a powerful weapon to kill 10,000 Ori followers.