Rodney is working with Zelenka to do a diagnostic on the Stargate, as it is working after Rodney tried an accelerated dialing program. They’re interrupted when something hits the city and they go to investigate. It’s an unknown probe with weapon damage on it. Rodney prepares to analyze the probe code and Major Lorne suggests that Zelenka continue with the gate diagnostic. Despite the fact that Zelenka agrees, Sheppard overrides Lorne and has Zelenka work on analyzing the probe as well. However, the system shuts down just as Rodney starts to get somewhere, but he sees enough to determine that the programming is nanite code. Rodney reports to Sheppard what he saw, despite Zelenka’s insistence that there was nothing there that he saw. There’s an explosion and Lorne reports that the probe self-destructed but nobody was there to be harmed. Rodney gets Sheppard off to the side and insists that something is going on.
Sheppard practices stick-fighting with Ronon and the two discuss the situation. Ronon agrees that both he and Teyla have noticed that people have been acting oddly. Ronon “accidentally” nails Sheppard over the right eye, leaving a cut, and tells him to go to the infirmary for stitches. Keller says he doesn’t have an injury and reveals that there’s nothing but blood. Sheppard wonders if he’s been infected with nanites and tells her to do a test. Keller says the test shows negative but Sheppard suspects that the retrovirus may be responsible and tells her to do a blood test. Keller agrees, but later secretly meets with Lorne and they decide to continue but to be careful.
Keller tells Sheppard the blood test was negative but Sheppard isn’t satisfied and has her run the test again. He gets together with Ronon and Teyla and they call Rodney in for a secret meeting. They cut Rodney’s hand and it heals instantaneously, the same way their hands healed when they tested themselves. They figure that Zelenka is in on it and crashed the computer as it worked on the nanite code. They access the infirmary computer but there are no blood test results. Sheppard and Teyla go to the infirmary to run another test while Rodney uses the life sign sensors and determines that they are the only four human beings in Atlantis.
Keller and Lorne notice the scanning and take security teams, while Rodney finds another life sign and Ronon take shim along to investigate. In the infirmary, Teyla and Sheppard determine they are infested with nanites, but Lorne arrives and holds them at gunpoint. Ronon and Rodney find the life sign: Elizabeth Weir. She wakes up but before they can compare notes Keller and her team arrive.
Sheppard tells Lorne to back down but the major refuses and tells Sheppard to shoot him if he feels he ha to. When Sheppard does, the wound heals instantly: Lorne and the others are Replicators. Keller reveals that when Rodney corrupted their code to turn them against the Wraith, they lost their programmed inhibition against duplicating living beings. Her group of Replicators are part of Niam’s batch that seek Ascension, and they used nanites to create their own humans from scratch based on the memories they took from Weir when she was captured by Oberoth and the main group of Replicators that are battling the Wraith. They have been using Sheppard’s team and Weir as an experiment to determine how humans reach Ascension.
Sheppard’s team and Weir are put in the brig and they confirm that Weir is what she says she is. Rodney figures out that the gate isn’t working because it’s not a real gate, and the sky has been maintained deliberately and abnormally overcast, which has kept them from confirming their location by the stars. Weir is then taken to the Replicator-Keller, which admits that Oberoth killed the “real” Weir several months ago when her mental influence proved too dangerous to keep within the Replicator consciousness. As part of Niam’s group, Keller and the others are trying to analyze and duplicate the human soul but since the experiment has failed, they’ll have to start from scratch. Oberoth and his main group have given up on Ascension, which is why they’re wiping out human populations to stop the Wraith.
Weir is put back in the brig and explains that Replicator Keller and the others will wipe the team’s memories, and the probe belongs to Oberoth and his group of Replicators. The experiment has been compromised and a Replicator Destroyer is on the way. Replicator Keller comes to eliminate them and Weir points out that it makes no sense to “reset” five human souls, as they’ll always figure out something is wrong no matter how they’re reprogrammed. Keller warns that Oberoth’s ship has arrived and the fake Atlantis doesn’t have enough power to maintain shields against it. As missile fire starts to rock the base, Weir and the others convince Keller to give them a chance. She releases them and gives them a sensor device that can locate all of the Replicator ships throughout the Pegasus galaxy. They leave in a clocked puddle jumper as the fake Keller, Lorne, Zelenka, and others are destroyed along with the fake Atlantis.
The duplicate team hitches a ride on the Replicator destroyer as it heads back to the homeworld. Once it gets there they determine that the Replicators have rebuilt their shipyards since the real Atlantis sabotaged them. They then steal a ship with hyperdrive and make their escape.
On the real Atlantis, Rodney is working on his streamlining program for the Stargate dialup when they get a message from an expedition: the duplicates have contacted them and are asking for a meeting. Sheppard takes his team to meet with the duplicates. The two McKays, eager to work with someone of equal intellect, start implementing the tracking program. The real Sheppard talks with the duplicate Weir, which wonders if anyone can accept them. Ronon and Teyla aren’t happy with the situation either. However, a Replicator destroyer arrives, having tracked the stolen ship. It opens fire and another ship cuts off the Stargate so no one can escape. The duplicates agree to provide a diversion and fly the Puddle Jumper off so the destroyer follows, and Sheppard’s (real) team makes their escape. The Replicators find that the duplicates have deceived them, and presumably destroy them for good.
Back on Atlantis, Rodney is working on the tracking system, trying to bury his grief after confronting Weir since resolving his grief. Zelenka tries to offer him some help in coming to terms with her death, but Rodney prefers to bury his grief with hard work. He finally gets the tracking device on-line and shows Sheppard that it has picked up a few Replicator destroyers. And then more. And more…
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