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.

When a "chosen" boy found on planet Abydos is brought to SGC, he sends a telepathic message, causing Daniel Jackson's personality to undergo disturbing changes. Will the rest of SG-1 be able to solve the mystery of the boy's origin before he becomes a power-hungry warmonger?