Sheppard's team is returning from a planet where they've discovered hostile flying monkeys. They approach the Stargate but there's a power surge in the Jumper and the pods don't' retract. They lose power and hit the Stargate then start to drift. McKay determines they have power but it's not getting due to the system. As the controls short circuit, McKay realizes they're in a failing orbit and their radio is off-line. One of the pods powers up but they lose life support. Suddenly everything comes back on line and they make it back to Atlantis.
Sheppard reports in to Woolsey then checks in with McKay and Zelenka, who say that there's nothing apparently wrong with the Jumper. Meanwhile, Woolsey takes a lift and the power systems fluctuate, delivering him to the top of one of the spires and trapping him there. Power fluctuates through the city and McKay confirms nothing spread from the Jumper. They lose power to the Stargate and the same electrical arcs shot through the area. Woolsey eventually gets back to central control just as the power goes out entirely except for McKay's computer. A message appears on the screen: "help." McKay asks who they're in contact with and the person at the other end types "elizabeth weir."
Rodney asks where "Weir" is and she says in the computer, and it's difficult to control. The power comes back up and "Weir" asks for help. Rodney and Zelenka merge all of the city's programs and patch in a voice synthesizer. Elizabeth talks to them and relates how she ordered them to leave her behind, and afterward the Replicators released the nanites in her body. Elizabeth managed to maintain her personality but the other Replicators sensed she was different. Oberon hunted down her and the other independent Replicators, until the Replicator homeworld was destroyed. She and the other heretical Replicators found a planet and attempted to Ascend. One of them, Koracen, argued that they should find a technological solution. He determined a way for them to project their consciousness into subspace at the cost of their physical bodies. However, Elizabeth reveals there was no next step and they've been stuck in subspace. The Replicators tried to find someone or some technology to help them, without success. So she broke away from the others, who were becoming increasingly bitter, and came to Atlantis to use the expanded computer systems.
The team discusses what to do and McKay suggests they use the Replicator machine that he created FRAN with. Woolsey refuses to take the risk and Sheppard suggests they upload her into a virtual machine. They're interrupted when Zelenka reports that Elizabeth is working in the laboratory with the Replicator machine. The doors are sealed but open to reveal FRAN. McKay concludes Elizabeth used the pattern of FRAN store din the systems. McKay deactivates the machine while FRAN/Weir explains that she is safe. Woolsey and Ronon are still suspicious and FRAN/Weir uploads schematics of the various alien technologies she's accessed. She asks for a chance to earn their trust.
The Atlantis systems are now stable and McKay suggests they keep her under constant guard and study. Woolsey still doesn't believe it's worth the risks but McKay insists that he owes it to Elizabeth. Woolsey refuses and goes with the plan to upload her into a virtual reality where she can prove herself without risk. Meanwhile, Teyla chats with FRAN/Weir about her son, who is off-world with his father. Sheppard comes in and explains how they have to be cautious. FRAN/Weir tries to reassure him but then declares that the other Replicators have found her and are on their way to Atlantis. They go over possible counter-measures and McKay writes the equivalent of anti-virus software to keep them out. Sheppard accuses FRAN/Weir of setting them up and she says the Replicators don't intend to harm them. The power systems fluctuate before McKay can finish his program. Communications go down and Zelenka goes to pull the Z.P.M.. One of his technicians is killed by an electrical discharge.
Woolsey and McKay establish contact with Koracen who insists that they want bodies. Woolsey refuses to give them access to McKay's machine and the Replicators cut off all means of departure from Atlantis. They then activate the ZPMs and the city starts to sink. As the city corridors start to flood, Woolsey has FRAN/Weir tell the Replicators to go ahead and sink the city, but they'll be trapped in limbo forever. FRAN/Weir warns they won't stop but Woolsey notes then they'll all die together. The Replicators shut down the ZPMs and the city stabilizes, and Woolsey prepares to negotiate. FRAN/Weir speaks with the other Replicators and they ask for human bodies. They'll need temporary Replicator bodies to create human bodies that they can transfer into permanently. Woolsey has McKay take the necessary precautions to keep the Replicators from causing trouble.
FRAN/Weir goes into the force field-sealed lab while Woolsey considers letting the human-Replicators leave. Sheppard wonders what happens if one of them wants to stay, but Woolsey defers that to later. The Replicators create their new bodies and go to work. However, several hours later Koracen breaks out of the lab using a timed program to disable the force field, tossing Ronon aside. Sheppard and his men confront the other Replicators who note that FRAN/Weir went after Koracen. They deny that they knew about Koracen's plan but Sheppard refuses to let them leave. He goes in pursuit and catches up to Koracen, who explains that he has no desire to take a human body and plans to pursue Ascension in his new form. Koracen throws Sheppard away and runs, while McKay determines that Koracen has cut off all power except to the Stargate so he can escape.
Sheppard finds FRAN/Weir, who wants to handle it on her own. Koracen arrives and says that FRAN/Weir was working with them all along and she's in command. FRAN/Weir admits she brought them there but didn't know Koracen would cause trouble. Sheppard doesn't believe she's Elizabeth any more. Koracen attacks Sheppard but FRAN/Weir attacks Koracen, inserts her hand into his head, and destroys him.
Later, FRAN/Weir meets with Woolsey and the others and says that it is too risky and she can't guarantee there'll be no further trouble. She offers to take the Replicators to another planet where they can conduct their research. She goes through the Stargate first and confirms for the other Replicators that it's safe. They go through as well… and find themselves floating in the depths of space. FRAN/Weir deliberately led them to their destruction rather than risk them causing harm to anyone else.