SG-1 returns early from a mission only to realize that they and Gen. Landry aren't on the same page as far as the the mission they've just completed is concerned. The confusion is quickly resolved when the "real" SG-1 returns at the correct time. Dr. Lam examines them all and concludes that they are identical and thinks they might be clones. Sam however thinks they may have come from a parallel universe as the result of the black hole they created when they destroyed the Ori beachhead. As more SG-1 teams arrive from other alternate universes, one of them includes Dr. Fraiser and another includes the Tok'ra Martouf. It's left to Sam and Martouf to find a way to send them all home.

Based on the information Vala gave them, SG-1 travels to the planet where Merlin may have hidden his secret weapon to defeat ascended beings. There they find an appropriately medieval village and learn that Merlin kept a library there. The locals have never been inside owing to a curse on anyone who dares enter, but SG-1 finds a way in. Once inside, they find a secret chamber that may reveal the location of the weapon. The SGC, meanwhile, has located the Ori's Supergate. Sam's attempt to get control of it is too late, and four Ori ships make their way through. In the ensuing battle, much of Earth's fleet is destroyed, and the future of several SGC members is left in doubt.

As the Ori invasion continues, Vala and Daniel must deal with their leader, Vala's young daughter, who is rapidly aged by the Ori to serve their purposes.

Martin Lloyd seeks out SG-1 for assistance when his failed TV show based on the real Stargate program becomes a feature film.