Exploring a strange and beautiful garden, SG-1 comes across a dome containing a race that are connected to machines. The team are captured by the machines and rendered unconscious, but awake to find themselves reliving pivotal moments of their lives, over and over again. Then they discover it is virtual reality and a mysterious keeper appears to persuade them to try different outcomes for the moments. But can the team escape his clutches, when they don't know what is real and what is not?

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.

After being rendered unconscious during an expedition, Carter's subsequently-ordered furlough is interrupted by a mysterious being with a message and growing affection for her.

SG-1 has changed the course of history and made the SGC virtually non-existent. Doctors Carter and Jackson have helped Brigadier General Hammond to find the Antarctic Stargate, but are not being allowed to help any further. They help Jack to power up the time machine, and he gets Hammond to allow them on the mission to Chulak to find Teal'c.