As the Goa'uld attack fleet approaches Earth, all four members of the SG-1 team are taken prisoner. They get help from an unexpected source when Bra'tac, Teal'c's mentor, reveals that he is on board. Apophis has delayed the attack until his son Klorel is revived, giving them some time to prepare. SG-1 has used all of the C4 on one of the two ships but must find a way to dispose of the second. Back at Stargate Command, Lt. Col. Bert Samuels arrives as a Pentagon liaison officer but also reveals a new weapon they have developed. General Hammond is dubious. They begin to transport humans to an Alpha site in order to ensure the continuation of mankind.

Martouf leads a Tok'ra delegation with crushing news for Carter: her father Jacob/Selmak has been captured by Sokar and imprisoned on Netu, an Egyptian name for hell, on a moon of planet Delmal, where prisoners are sent to suffer eternal torture, and from where no one returns; only Jolinar has ever escaped. SG-1 mounts a rescue operation with Martouf, top-priority being any information Selmak can offer about Sokar's plan to subjugate the other system lords, an unprecedented threat for all humanoids in the galaxy. Teal'c must pilot a Goa'uld ship and keep it in orbit as landing is impossible except by small pod, but first Martouf taps into Jolinar's memory, which is partially blocked by some trauma beyond physical torture. Only when they're down and in the custody of Netu's lord Bynarr, does Sam realize he is the key, in a 'personal' way, but not voluntarily, as she had thought. Sokar learns of their presence from Bynarr and orders the team and craft destroyed, but this also means there must be a way out. Bynarr's prime, Na'onak, has, and is himself, a major surprise.

Ready to go on vacation, O'Neill is beamed away by the Asgard. Thor tells him that Earth is faced with an enemy even worse than the Goa'uld.

On a routine mission, SG-1 encounters a civilization desperate to be freed from the clutches of a Goa'uld. While on the planet, Jonas falls ill and is suspended from active duty. His mysterious illness is diagnosed as a brain tumor but gives him the unbelievable ability to glimpse the future, a future where O'Neill and SG-1 are walking into a trap!

The SGC is approached by an Al'kesh bomber which lets itself be taken down, so they can capture Ba'al, who offers to exchange the necessary information to find Merlin's weapon for human help to eliminate his clones, which want to kill him. They mistrust his story, as does NID Agent Malcolm Barrett, who, however, fails to take over the investigation. Since the captive might actually be a clone, several missions to different planets retrieve and capture all clones, but which is the real Ba'al, and what are his true intentions?