Colonel Jack O'Neill is brought out of retirement to lead a new expedition back to Abydos, only to find an old friend, a new enemy and a far wider use of the Stargate.

The Stargate team must justify the project's continuation when a doubtful senator, Head of the Congressional Military Appropriations Committee, comes to review the project's performance.

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.

With the threats of both the Replicators and the Goa'uld greatly diminished and the sister ship to the Prometheus, the Daedalus, now under construction, SG-1 is anxious to get a ride on the new ship. However, the mood is somewhat darkened by a phone call informing Dr. Jackson of Catherine Langford's death. After the funeral, Catherine's niece gives Daniel "a few odds and ends" that her aunt wanted him to have. Upon delivery it is discovered that almost her entire collection was shipped to Daniel's lab. He finds in one of her books a possible location of a ZPM, but scans of the area showed that it was no longer there. Daniel proposes that they use the Ancient's time machine to take it from Ra at Giza in 3000 BC.