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.

While O'Neill and Carter head to Washington to be decorated by the President and find a security leak, Jackson and Teal'c go to Abydos (after they unbury their stargate) to see Sha're's father. They arrive to tell him that they have been unsuccessful in finding Sha're, only to discover that she is already on Abydos. But they find that she is pregnant by Apophis and the baby holds the secrets of the Goa'uld.

Responding to a help cry from Kasuf, SG-1 and more USAF wipe out a Goa'uld Jaffa guard to save most of the slaves on Abydonia. When Amaunet turns her hand device on Daniel, he can't bring himself to shoot his beloved wife Sha're, but Teal'c saves him by fatally staff-shooting her, and Abydononian funeral tradition squashes his hope of a sarcophagus resurrection. Crushed by grief, Daniel has apparitions of Sha're and, once released from hospital, resigns from SGC claiming the quest for his wife was his reason to join. Daniel's former research assistant, Dr. Robert Rothman, succeeds him in SG-1; but Jack is sure he'll be back. Sha're (or Amaunet's posthumous manual spell?) keeps appearing to Daniel life-like, telling him to forgive Teal'c and together find their boy who, as Harsisis, has all the Goa'uld knowledge in his genetic memory, which, to the Goa'uld, means he must be killed. Daniel agrees to return, but has a secret agenda, too.

A group of nomads on an alien planet find Daniel Jackson naked in the middle of ruins and take him in. Jonas translates the tablet Daniel said was important and discovers that it describes the last city the Ancients were building before the plague. He surmises that the list of addresses Jack put into the computer while storing the Ancient data were Ancient outposts in temporal order. Thus the last of the addresses should be the "City of the Lost". SG-1 visits the planet and happens upon the nomadic people, now inhabiting the ruins of the Ancient city. There they find Daniel, but discover his memory is gone. They must recover his memories in order to discover the secret to defeating Anubis.