A strange woman seems surprised to find herself in a hallway within Atlantis. She goes to an auxiliary lab and Dr. Zalenka greets her, seeming to recognize her. She appears confused and he suggests he take her to the infirmary. When he insists, she grabs a knife and stabs him, then look in a nearby mirror... and finds herself with Dr. Keller's face.
The woman goes to the inhabited areas of Atlantis and looks out from a balcony, then tosses the knife away. Rodney comes up and, believing she's Keller, wonders why she missed their lunch date. He says he tried to contact her on her headset but she didn't respond, and the woman says that it must be malfunctioning. Paranoid, he wonders if he did something wrong. He's interrupted when the woman gets an emergency call on the headset. Rodney wonders why it's working now and activates it. Zalenka has been found and taken to the infirmary for surgery. The woman has no choice but to go there but when she's called upon to operate, she fakes being ill and leaves the other medical staff to save Zalenka.
Rodney and Sheppard report to Woolsey that Zalenka is recovering but is in a coma and unable to identify his attacker. Rodney talks about "Keller" seeming ill. Woolsey says he'll have Beckett examine her when the doctor gets back from his current mission.
The woman goes to Keller's quarters and goes through her belongings. Ronon comes in to see how she's doing, but quickly notices she's acting strangely. When Rodney comes in to inform the woman that Beckett will be back, she acts confused and both men realize something is going on. Beckett arrives and gives the woman a full scan, but doesn't notice anything odd. He concludes it may be simply a psychological problem rather than an illness and orders a sedative.
That night, the woman sneaks out of her quarters and finds her way to the jumper bay. She gets a gun and tries to work out the controls, but Rodney has followed her there and wonders what is going on. She claims she was just going for a flight but he notes she doesn't have the Ancient gene. She tries to seduce Rodney into flying them to the mainland for a picnic under the stars, but Rodney realizes Keller isn't that vampy. He refuses and she draws the gun on him. She prepares to shoot but Ronon, figuring something was wrong, stuns her from behind.
The woman is confined in the infirmary and Beckett wonders if she simply snapped, and possibly attacked Zalenka. Sheppard interrogates her and confirms she attacked Zalenka. The woman identifies herself as Neeva Cosol and says he and her two associates were looking for artifacts in a village vault. They broke in and she activated a device, along with several black stones. She put one in the machine and found herself in Dr. Keller's body on Atlantis.
Going from Neeva's description, Rodney identifies the device as an Ancients communication terminal. SG-1 found a similar device several years ago and Vala and Daniel switched bodies. He figures that Keller came into contact with similar black stones in his laboratory, and when Neeva inadvertently activated the terminal it transferred her mind to Keller's and vice versa. Unfortunately, there's no guaranteed way to break the length.
Keller is on a planet, being held by the local villagers in a cell. The Magistrate visits her and tells her that they've checked her record and she's wanted for murder and theft on other planets in the Coalition. They plan to continue searching for her associates, but she's to be sentenced to death.
The team prepares to find Keller on the planet, and Neeva tries to bargain. Sheppard refuses and only guarantees her safe passage once they reverse the transfer. Beckett warns that if one or the other is killed, the other woman will be trapped in a different body. They go to the village via Stargate but the surrounding forest is too dense for a puddle jumper so they head on foot to the village. They arrive at the village and talk to the Magistrate's second-in-command. She's suspicious of showing them the device and says they'll have to talk to the Magistrate after the execution. Realizing whose execution it is, the team heads out.
The Magistrate and his men take Keller to a clearing and prepare to decapitate her. Neeva's associates, Bordal and Jannick, arrive and open fire on the guards. Keller runs into the woods and the two accomplices find her and untie her, then make their escape. Sheppard and the others arrive and overhear the Magistrate ordering a search and a sentry on the Stargate. Ronon starts tracking Keller and the men. The two men take Keller to a cave and demand to know how they're going to get off the planet, and expect her to come up with a plan. Keller tires to make the best of it without much luck.
In the woods, Neeva make a break for it and evades Ronon in the woods. She gets to the cave and tries to explain what happened. Even after she tells them things only she would know, they don't believe her. Neeva insists they shut down the device and undo the transfer, but the men decide to head for the Stargate instead. As they go there, the village guards ambush them. Bordal is killed and Keller (in Neeva's body) runs away. Jannick prepares to shoot her but Neeva in Keller's body tries to stop him. A villager shoots her and Jannick goes after Keller. Ronon arrives in time to stun the guards and they take Neeva-in-Keller to the Magistrate's house. Beckett prepares to operate to remove the bullet while Sheppard and Rodney demand to see the Ancients terminal. The Magistrate agrees and Rodney tries to figure out how to shut it down.
Jannick catches Keller and prepares to explain her despite her explanation. In the village, Rodney can't figure out how to shut the device, but notes SG-1 destroyed it by throwing it into the event horizon of a Stargate. They have no choice but haul it back to the Stargate, but Ronon simply shoots it. Keller wakes up in her own body. Neeva finds herself confronting a loaded gun and tries to convince Jannick she's the real Neeva. Unimpressed, he starts to pull the trigger...
Later back on Atlantis, Woolsey tells Rodney that they haven't found Neeva but the Coalition will continue their search for their criminal. Rodney stops in to visit Keller and makes much over her gunshot wound while ignoring Zalenka's complaints. Zalenka gets Beckett to wheel him away, cursing. Rodney suggests that when Keller is feeling better, they take a picnic trip to the mainland and she wonders if he's had his personality switched.
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