Sam is working on Merlin's phasing device when Mitchell comes in to check up on her and runs afoul of a protective force field she (forgot to) put up. There's no news on Daniel and he invites her to lunch, but she wants to run one more test. She puts the force field back up and as Mitchell watches from the galley, she activates the device… and disappears. She fails to reappear on time, and wakes up to find herself in SGC but to her, Mitchell has vanished. She drops the field and Lee rushes in and addresses her as Major. Major Lorne also comes in when he's supposed to be on Atlantis, but now he's the leader of SG-1.
Lorne reports to General Hammond, who is in charge, and explains that Sam is from a parallel dimension. They interrogate her and Sam tries to find out what was going on in the lab in their world. Daniel is still captured by the Ori, Mitchell quit the military, Teal'c went back to the Jaffa, and Vala is under arrest in Area 51. She asks to see the surveillance footage and Hammond agrees to let her see it.
The footage shows that this world's Sam was working on capacitors to extract energy from parallel universes. Major Carter found a way to open the gate for a split second, taking energy from thousands of universes for only a microsecond at a time. Sam concludes that since she was out of phase at the time and protected by a force field, the interactive experiments pulled Sam through. However, she doesn't know what might have happened to Major Carter but believes they weren't switched. Hammond speaks to Sam and reveals they fought off one Ori ship that attacked Earth, but it exhausted their ZPM and they haven't discovered Atlantis. Three years ago in this dimension, Anubis launched an attack and the U.S. revealed the existence of the Stargate program, people panicked, and the President declared martial law. The world's government reacted in a hostile manner toward the U.S. They want Sam to complete Major Carter's research and agree to give her access to the base's resources to try to figure out a way back to her dimension, in return for her help for them. Hammond warns that the Ori are assembling a fleet for a full-scale attack on Earth within the next five days.
Later Sam tells them she plans to pursue her own line of research and puts herself and her equipment out of phase, then bringing it back into phase. She plans to hide the entire planet. They agree to let her continue and later she talks to Lorne about a photo she found of Major Carter with a wedding ring. It turns out Major Carter was married to McKay.
Sam tells Hammond that she can't meet the power requirements but Hammond takes her to the briefing room where she meets with the U.S. President: Hank Landry. He agrees to let her have most of the U.S.'s power output then gives a speech to the American public assuring them it's necessary. Lee and Sam work to use the power while the Ori fleet approaches. Power grows out across the continent as the Ori ships enter orbit… and the Earth disappears. The Ori ships open fire but the beams just pass through the de-phased Earth.
Later Landry thanks Sam and introduces her to the press as a hero. She is feted while Lee tells her that they can't replicate the experiment without controlling the environment on both sides of the bridge. Sam is uncomfortable with standing in for Major Carter and they're interrupted when a protestor comes in demanding freedom and is brutally tortured on the way out. Sam is teleported up to the Prometheus with Landry, as the spaceship now serves as Air Force One. Landry is fairly comfortable with the fact he's had to deliver martial law. Later in her lab, Sam reviews newsreels of the American government bombing terrorists in Irish, as well as reports of the Americans abandoning the Jaffa. Hammond supports Landry even though Sam warns that the threat will never go away.
Sam goes to visit Major Carter's ex, Rodney McKay, and reveals she's not his Major Carter, then asks for his help. Meanwhile Lee has uncovered the Glastonbury device but admits to Landry and Hammond that they need Sam to operate it. Landry plans to make sure that Sam can't return to her home universe, over Hammond's concerns.
Rodney agrees to help her but when Sam returns to the lab she discovers that her equipment has been transferred to Area 51. Landry tells her that they'll reassess the matter after he's reaffirmed as President, and he wants to use her to bolster his image. Hammond still isn't happy with the situation and warns it'll be tough to go back. Meanwhile Sam realizes that Landry's Secret Service are watching her and they'll run an anti-trust investigation against McKay to keep Sam in line.
Sam goes to see Mitchell, who is in a wheelchair and living in a cheap apartment. He reveals that Landry used him for PR but dropped him when he questioned the system. Sam calls into the Secret Service and agrees to cooperate. During her first live news interview she speaks out against Landry until they cut her off. McKay warns her that the government won't let her get away from it and Sam discovers that the government has suppressed all news of the incident. As she leaves the Secret Service take her into custody and escort her to Landry aboard Prometheus. He tries to convince her that her own world would do the same thing but she notes that her Landry wouldn't do it.
Back at SGC, she discovers that McKay has been hired as her replacement and is working with the Glastonbury technology to create an interstitial bridge to send Sam back to where she came from based on Landry's orders. Sam tries to convince McKay about the danger that the rest of the galaxy faces and suggests McKay work on him. A little later Sam returns to her own dimension and greets "her" team, who admit they talked to the empty room to keep her company, as Sam admits it's good to be home.