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 team, now designated SG-1 are planning their next foray through the gate as they try to map out the variety of sites available to them and locate their missing friends. O'Neill asks that Teal'c be allowed to join his team but Gen. Hammond thinks that will be unlikely given that he is the host for a Goa'uld. Unknown to anyone, however, is that O'Neill's close friend, Maj. Charles Kawalsky, leader of SG-2, has been infected by a Goa'uld, an immature version that has not yet taken complete control of the host. Kawalsky is having regular blackouts during which the Goa'uld is trying to return to the gate. An MRI reveals what is wrong but it's unlikely the creature that has fused itself to Kawalsky's spine can be surgically removed. Meanwhile, Col. Kennedy arrives to question Teal'c who has pledged his loyalty to his new world.

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.

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?

Alternate reality versions of Kawalsky and Carter are caught at Area 51 after coming through the quantum mirror.

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.