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.

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.

Bra'tac and Teal'c encounter a heavily armed enemy with shielding protecting him from Goa'uld weaponry who took out two Goa'uld personal guards. They barely manage to defeat him and bring him back to SGC for study, but this new threat poses a greater problem for the Tau'ri.

With a new commander of the SGC comes a new leader of SG-1, Lt. Col. Cameron Mitchell, a former fighter pilot who flew an F-302 in the battle over Antarctica. However, he is deterred by the fact that all the other members of SG-1 are leaving for other ventures: Teal'c to manage the Jaffa Nation, Carter to Area 51 for alien R&D, and Dr. Jackson to Atlantis as an Ancient expert. Mitchell endeavors to keep the members of SG-1 for himself, but they are increasingly tough to convince.