The team gets an unscheduled off-world activation and here's an unusual name, and Landry confirms they get SG-1's code. The team comes through normally and reports nothing unusual. However there are a few discrepancies in their report – they think Selmac is alive and the planet was ruled by a different Goa'uld. Then they get a second gate activation from SG-1, at the time they were supposed to return. They open the iris and…a second SG-1 comes through.
Landry figures Ba'al and his cloning technology isn't involved, and that the first team are the "fakes." Sam believes the new team is from a parallel/alternate universe, but can't explain how they got there. Mitchell talks to Daniel (henceforth Daniel-2) who suggests their "originals" may be up to something. Mitchell-2 notes that there have been examples of "fake" SGCs in the past. Sam finds an unidentified energy spike and continues to run tests, and both Sams conclude a black hole is responsible, the one the Ori created in their first beachhead attempt. Then they get a Gate activation and another SG-1 ID code. Mitchell at the other end says they're under fire and Landry reluctantly lets them through.
Sam concludes there is now a ripple effect across several parallel universes and all the wormholes passing by the black hole are leading to the "core" SGC's Earth. Lee and Sam try to pin down the original energy spike and Sam calls in Sam-2. Landry is only letting through the teams that are in danger, and some have some unusual twists. One team has Dr. Fraiser as a team member, much to Teal'c and Daniel's astonishment, and they reveal to her that "their" Dr. Fraiser died two years ago. Sam (now working with a lot of other Sams) concludes the travel is escalating the damage and that even if they had the quantum mirror they couldn't return everyone back. An alternate Martouf also comes through with one of the teams and helps her. Dr. Fraiser reveals that in her world the Ori are ravaging Earth with their plague.
Martouf reveals Sam is with someone else in his universe, but before he can answer another Sam determines the "core" Earth's gate is locked to the black hole due to an energy source, and they have to find the point of confluence and recreate the circumstances of the random energy surge. They can disable the Stargate…but it will strand the teams already on the core Earth. Now all they have to do is deliver an explosive device to the singularity. They contact an Asgard, Kavasir, who brings a time-dilation device, but he's not confident of the chance of success. Landry orders them to go ahead, and Martouf tries to reassure Sam that she'll have to do what she has to for her Earth.
Fraiser meets with Landry and asks him to postpone the mission for the sake of all the different Earths, but Landry is forced to choose his Earth. SG-1 prepares to leave for the black hole on the Prometheus when the original new batch of arrivals show up to go with them. It becomes clear that Sam-2 and her team are working to sabotage the mission.
The alternate team make their move with captured zat guns, and Teal'c-2 knocks out Mitchell. The rest of SG-1 are taken prisoner and the alternates take a three-week detour to Atlantis. Later Mitchell asks to meet with his counterpart, who reveals they need the Atlantis ZPM to power up the Ancient weapon in their universe, and that they have a way back to their universe and planned the whole thing. Sam gets them out of the cell by finagling the circuits and they head for the armory. Mitchell and Teal'c go one way and "Mitchell" reveals he's Mitchell-2. But Daniel and Sam get the drop on them, revealing they knew he was up to something, and lock up their counterparts.
SG-1 reports back to SGC and gives them an update – Sam has figured a way to return everyone to their correct Earths. Using a directed energy weapon borrowed from the Asgard, they fire a burst which creates a stable wormhole leading back. The alternate SG teams go back, and they give the Ori plague cure to Fraiser and Martouf for their Earth.