While testing new technology, a UAV malfunctions and crashes on a planet. SG-1 goes to determine the cause of the malfunction, but discovers that their presence may be causing serious injury to the planet's primitive inhabitants.

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.

A solar flare sends SG-1 back in time thirty years to 1969. Captured by military police at Cheyenne Mountain, they escape with the help of a young Hammond and then must find the Stargate so they can return to the present.

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.

Now that Apophis has revealed himself, he promises the prisoners to overturn Sokar, which requires extracting an irresistibly valuable secret, to which end he drugs Sam with the truth serum 'blood of Sokar.' Apophis also implants a memory device in, and gives the drug to, Jack to torture him using the persona of his young son that died, and Daniel for the location of his Harsesis son. Martouf's love for Jolinar makes him betray that the Tok'ra are on planet Entac - a convincing lie, so Apophis's plan to earn Sokar's gratitude, and then kill him when rewarded with the lordship of Netu, is on a shaky basis. Teal'c must help the Tok'ra Aldwin prepare a nuclear weapon to explode the whole moon when his ship arrives as their last chance to eliminate Sokar, but he decides to rescue SG-1 instead, by flying in the path of the rings device on Sokar's ship when he arrives.

The SGC send a MALP to a huge pyramid and inside they discover a crystal skull like the one Jackson's grandfather found many years before. SG1 visit the planet and whilst Daniel is looking into the eyes of the skull, as his grandfather did, an energy field envelops him. Teal'c fires his Zat at the skull, but Daniel has disappeared. Carter collapses and the team minus Daniel return to the SGC. Teal'c returns to collect the crystal skull, but will he be able to find Daniel?

Col. O'Neill and Teal'c realize they and their friends are trapped in a time loop.

Teal'c is on his home planet, Chulak, where there is rebellion among the Jaffa warriors. He is betrayed as a sacrilegious shol'va (traitor) by Rak'nor, son of a Jaffa friend of his father, and handed to Terok, the torturer of system lord Heru'ur. Ignorant of his fate, the other SG-1 members join Jacob in a risky attempt to take hold of a space mine using a Tok'ra ship piloted by Jacob. En route to Apophis' spaceship, the expedition finds out that Teal'c is being offered as a confidence-building present from Heru'ur to cement an alliance with Apophis against the other system lords, which would make the Goa'uld threat more dangerous than ever. They decide to save Teal'c, but their attempt fails. However, Teal'c's resistance to torture and clear conviction that Goa'uld are not gods finally convinces Rak'nor, who now bravely acts.

On Juna, SG-1 gets a hostile welcome from the local warriors' leader Darian, who seems incredulous they even dared to return. They loyally deliver Sam and Teal'c to Cronus and told them to bury the Stargate. Cronus orders Darian to decapitate Daniel by staff weapon- to find his head is robotic. Cronus's obvious astonishment makes Darian doubt his divinity. At the SGC, Harlan urge them to go on a mission. The master robot-creator tells SG-1 that the robot versions of them he created need to recharge after 48 hours. In order to prevent the Goa'uld gaining access to their duplicates' memories, SG-1 reluctantly go to Juna. Darian now joins them, but feels most of his people won't dare challenge Cronus. The two Teal'cs concentrate on revenging the original's father by attacking Cronus recklessly, while the Sams and Jacks deal with the military problems and overthrowing the Goa'uld rule.