Rodney is chatting with Sheppard about how she doesn't trust him after he accidentally dropped her baby. They get to the control room where the technicians have picked up an incoming ship that appeared in orbit with no sign of a hyperdrive. They confirm its signal as belonging to the Daedalus, despite the fact it's supposed to be on course for Earth. Further, they scan it and determine no one living is on board.
Sheppard takes his team out on a Jumper while Atlantis confirms that SGC is tracking the Daedalus heading toward Earth. As they examine the ship they find signs of weapon damage and pick up an unidentified energy reading. Going on board, they find there are no F-302s and only one Jumper. Splitting up, Sheppard and Teyla go to the bridge while Rodney and Ronon go to Engineering. Rodney reestablishes power while Teyla brings up the ship's log. On it, a Colonel Sobel, the ship's commander but someone they've never heard of, notes that the crew is taking all of their supplies and abandoning ship to a nearby inhabitable planet.
The unknown energy reading continues to increase and the Daedalus… vanishes. Sheppard's team loses contact with Atlantis and vie versa, and Rodney determines that the ship has an unknown drive system that activated on its own. He identifies the energy signal as the same one that accompanied the arrival of his counterpart from another dimension. The drive shifts the Daedalus through parallel universes without moving it in space.
Sheppard and the others find four corpses: Ronon, Teyla, McKay, and Sheppard. They bag the buddies but due to the low temperature on board are unable to determine how long they've been dead. Rodney checks out his counterpart's computer and discovers that they weren't the original owners of this Daedalus. It appeared in orbit above their Atlantis and it universe-shifted when they went to investigate. Unable to stop the drive or reverse it, they starved to death due to lack of supplies. Rodney locates the chamber containing the alternate-reality drive and tries to decipher its workings. However, he isn't confident he can accomplish much since his counterpart couldn't either. Teyla and Ronon look for supplies and Teyla wonders what happened to her son in the universe of her dead counterpart. Ronon reassures her as best he can that there are millions of alternate universes and there's no way they can worry about what happened in all of them.
Rodney figures out that another of his counterparts created the drive and that it uses ZPM levels of power. It regenerates energy on its own and there's no way to stop it. The energy builds up again and they shift into another universe, where an alien ship of unknown design and markings is firing on Atlantis. Sheppard decides to help them and opens fire, disabling the intruder's weapons. It launches fighters and Sheppard and Ronon try to hold them off. The sublight drive is damaged but Rodney manages to increase the drive efficiency so they jump faster. They shift away from the fighters just as several of them crash into the hull, but find themselves dangerously close to a red star.
As the temperature increases, Rodney tries to determine why they're closer to the sun when they shouldn't have shifted physically. He realizes that in this reality the star expanded much sooner then in their reality (the reality that Sheppard saw when he traveled to the future). Rodney reroutes power to the shields but can't predict how long they have until the next jump. While the others reroute the power, Ronon hears a noise and goes to investigate. An unknown alien soldier attacks him. He manages to fire his gun, drawing Sheppard and Teyla's attention. Sheppard goes to check it out and opens fire. It takes his and Ronon's combined fire to kill the alien solider. It is wearing the same markings as the alien ship in the previous reality. They figure the alien boarded when the fighters crashed. Other aliens have also boarded and open fire. Sheppard and Ronon try to hold them off. Meanwhile, Rodney warns that the shields won't hold against the temperatures and they can't move due to the sublight drive damage. He has Teyla drop the shields and reroute the heat into the jump drive. They shift dimensions again while Sheppard and Ronon defeat the aliens. Rodney warns that they've overtaxed the jump drive and they only have a few jumps left before it's damaged beyond repair.
In this universe, Atlantis was destroyed and all that's left is an asteroid field. Using his counterparts' computations, Rodney figures a way to reverse their flight path, but they'll have to deal with the dangers in each previous reality. He uses the maneuver thrusters to put them into a higher orbit so they won't shift so close to the red sun in the previous universe. He and Teyla start working on the sublight drives so they can evade the aliens from two universes back.
They shift back to the red sun universe and try to compete the repairs. Teyla thanks Rodney for refusing to give up and he assures her he'll get her back home. The jump drive shifts them again before they can repair the sublight drive. The alien ship launches more fighters and Rodney gets the drive working just in time. However, it's not sufficient to outrun the alien attackers. Ronon and Sheppard try to hold them off without much success, but Atlantis in this universe launches F-302s that take out the fighters. The Atlantis flight commander is… Sheppard, who wishes them luck. They jump again and head for the docking bay to prepare to evacuate in the Jumper. However, one alien soldier has survived. He injures Rodney before Sheppard and Ronon can kill him. When he goes down, he activates a self-destruct device that takes out the entire passage to the docking bay.
Because they left orbit to evade the alien fighters, they'll be too far away from Atlantis when they make the shift to "their" universe. They can't destroy the jump drive once they return to their universe without risking the creation of an enormous space-time rift that could destroy the entire system. With time running out, they try to come up with a solution.
On Atlantis, Lorne and Zelenka detect the Daedalus when it arrives. They take out a Jumper but can only watch as the Daedalus jumps again. However, they detect four life signs in space: Sheppard's team put on space suits and evacuated the Daedalus before it jumped.
Later, Rodney is resting in the infirmary and considers making an improved version of the jump drive. Sheppard tells him not to. Teyla arrives and, trusting Rodney, lets him hold Torren.