Olivia, Broyles, and the Bishops arrive at a secret U.S. government facility. As the soldiers check their IDs, Walter asks for some gum. Inside, Nina is meeting with the head scientist, Dr. James Falcon, who is reporting that he's achieved no response yet. She goes to meet with the team, and Broyles explains that they've broken the encryption on Bolivia's laptop, thanks to Peter's work. However, the vital information is buried among all of her mundane observations on This Side. They see the assembled device for the first time, which stands over two stories high.
Dr. Falcon starts to give them a status report, but Walter realizes that Falcon works for him and introduces himself. The scientist explains that there's no indication that the machine can hold or transmit any kind of power. However, the scientists notice an electromagnetic spike. Their computers start to short out. Meanwhile, Nina explains that Bolivia stole the key piece, but is interrupted when the device triggers. As they watch, Peter notices that he's bleeding from his nose, and tells them that his presence is what triggered it.
Peter returns home late at night and tries to avoid waking up his father. He goes to the refrigerator and makes himself a sandwich. Walter comes down and Peter claims that he was in the house and came down to get something to eat. His father asks how he's doing, and admits that he hasn't been able to sleep. He's been going over the First People book, but hasn't found any answers. Peter tells him to stop because he can't protect his son from everything, and offers Walter a sandwich.
The next day, Falcon prepares to test Peter using radiation. Walter objects and threatens to fire the scientist. When Nina intervenes, Walter takes her aside and admits that he's worried about Peter, and he wants to see Bell's notes on what he removed from Walter's brain. Walter insists that the only way he can help Peter is to become smarter. Nina reluctantly agrees to gather the information. In the lab, Olivia comes in to greet Peter, who insists that he's fine. She asks where he was the previous night when she called, and he claims that he went for a walk. Falcon says that they're ready and warns that it will take a while. He leaves with Olivia and they begin the radiation scans.
At the Massachusetts Port Authority, a man goes for a smoke and notices dead fish in the nearby koi pond. When he looks closer, he discovers a dead body in the water.
Broyles arrives at the lab and discovers Astrid working alone. He explains that he wants her to go over the information that Bolivia gathered and determine what is important. However, Broyles explains that Bolivia's log had a number of personal recordings about her and Peter, and he needs Astrid to be discrete. She readily agrees, and Broyles gets a call summoning him.
Walter examines the data from Peter's scans and worries about a minor myocardia. He tells Falcon to remove his son immediately, but Falcon believes that they need more tests. Olivia tries to intervene but gets a call from Broyles. She goes to the Port Authority, and Broyles explains that the dead man is Michael Baird. The fish died of mercury poisoning, meaning that "Baird" was a shapeshifter. His storage disk has been removed, and they wonder why someone would kill a shapeshifter. Olivia wonders if Walternate sent over someone to eliminate the remaining shapeshifters before they could find them. Broyles calls Astrid and tells her to check Bolivia's data files for references to Baird. He's on a list of thousands of Port Authority employees, and Broyles tells her to cut the files off from any outside access. When Olivia wonders what's happening, Broyles explains that Walternate must have a mole who knows they have the data file and told him.
At Massive Dynamic, Falcon tells Peter that all of the test results show no connection between Peter and the Device. Peter doesn't believe it, and Falcon insists that there's nothing from a medical standpoint. Walter comes in and tells Peter what Broyles and Olivia have discovered.
At Harvard, the team meets and Broyles assures Peter that they've questioned everyone who had access to the data files. Astrid admits that there are too many names to readily determine who is a shapeshifter. When Olivia asks if they can help, Astrid says it isn't a good idea, and Peter realizes that a lot of the information is about her. He leaves for Massive Dynamic and Olivia goes with him.
At Massive Dynamic, Brandon is interviewing one of the suspects, FBI Agent Matthew Nicholas Goldin, and takes a blood test. They're using a sophisticated lie detector created by Bell to determine if he's lying. Peter says they need to keep every suspect in custody until they confirm which one is the mole, surprising the others with his ruthlessness. Nina then talks to Walter privately and says that she found three DNA vials that Bell set aside, and that will let Walter regrow the missing parts of his brain. However, Nina warns him that there are three vials, and the labels were destroyed. Two of the vials belong to the rat and the chimpanzee that Bell used as test animals. Walter starts sniffing one of them, and Nina says that Peter needs professional help. In response, Walter insists that he's the one who needs to help his son.
Olivia and Peter watch as Brandon interviews another suspect, and Olivia tells Peter that she wants to read the files, no matter what personal information it contains about Peter's sexual relationship with her imposter. Peter explains that Bolivia would have considered him a fool, and he doesn't want Olivia to see him like that or have to read about it. Brandon finishes with the last suspect, but Olivia suggests that Falcon might also be a suspect. Brandon calls security and learns that Falcon left work early. Olivia and Broyles take a FBI team to Falcon's home and find the shapeshifter, dead, shot in the head with his data storage unit removed.
Astrid confirms that Falcon's name was listed on the data file, while Walter tests his own IQ. At the crime scene, the techs don't find anything, and Olivia worries that they're always one step behind.
Later, Walter prepares to dissect the Falcon shapeshifter, and comments that he'd like a banana despite the fact he doesn't like bananas. Walter asks what Bolivia said about him in her files, and Astrid says that Bolivia liked him. As they examine the body, Walter bares his teeth, much to his surprise and Astrid's. He realizes that he's displaying dominance, and concludes that the sample he took was from a chimpanzee. Astrid wonders if it's dangerous, but he assures her that his immune system will eliminate the foreign DNA. Walter notices something on the shapeshifter's fingers: blood.
Peter and Olivia discover that the killer broke in, meaning he and Falcon were strangers. Olivia then apologizes, saying she hasn't considered what Bolivia did to him. She assures Peter that her imposter is gone and they can get past it. Peter smiles and thanks her, and then gets called back to Massive Dynamic for more tests. He asks Olivia to tell Walter that he'll be back late and thanks her. After he leaves, Astrid calls to tell Olivia that they've confirmed the blood is A Positive. Brandon Fayette is the only person at Massive Dynamic who has that blood type.
In the streets, a woman is desperately running away from someone. She ducks through an empty building and a homeless man asks her for change. The woman, a shapeshifter, breaks his neck and then duplicates his form.
Olivia, Nina, and Broyles go to confront Brandon in his lab. They draw their guns on him, and he appears to have no idea why the suspect him.
The shapeshifter completes its transformation, but a man emerges from the shadows and shoots it dead: Peter.
A Massive Dynamic tech interrogates Brandon, and the lie detector confirms his denials. Olivia goes to the lab and tells Olivia what they've discovered, and starts going through the data files. When Astrid hesitates to help her, Olivia says that what's in the files are in the past, and they need to focus on the future. Astrid says she's been through the information, but Olivia figures that since she thinks the same as her counterpart, she'll see a pattern that Astrid hasn't.
At home, Walter is making a banana split when the phone rings. It's Nina, who says she was calling for Peter. Walter is surprised, since Peter had told Olivia earlier that he was going for more tests. He says nothing further, and Nina mistakes his silence for concern about his son. Walter goes to Peter's room and finds a list of names, including Baird's and Falcon's.
That night, Peter is watching the home of one of the shapeshifters, who is posing as Zach Alpert
At the lab, Olivia realizes that Bolivia had come to view Peter as good, and was starting to have real feelings for him. She realizes that the two of them think the same way, and asks Astrid for the original printout. They go over it and Olive realizes that it's a substitution code based on her childhood nickname, Olive. They confirm the existing shapeshifters, and the last one is Zach Alpert.
Peter breaks into Alpert's apartment and finds the shapeshifter watching TV. He shoots him in the back and then moves in to confirm the kill… only to discover it's a dummy. The shapeshifter knocks him down and says that he's been expecting Peter. He asks how Peter found him, and says that he knows who Peter is. The shapeshifter admits that he isn't allowed to kill Peter, but that won't stop him from using torture. Walter comes in, giving Peter the opportunity to get the drop on the shapeshifter. He cuts off the shapeshifter's fingers when it goes for the gun, and then shoots him in the chest as Walter stares in horror.
Olivia heads for Alpert's home and calls Broyles, and tells him what she's discovered.
At the Alpert apartment, Walter explains that he saw Alpert's name in the file on Peter's desk, and got his address from the phonebook. He stares in horror as Peter cuts out the shapeshifter's storage disk, explaining that he has to know what they know. Walter says that Peter isn't himself, but, Peter insists that the shapeshifters are inhuman soldiers, and he's not doing anything wrong. He shoots the shapeshifter in the head, and Walter asks why he didn't tell them if he thought he wasn't doing anything wrong. Walter insists that Peter has changed. Olivia calls to tell him that she's on the way to the Alpert house.
Broyles and Olivia arrive at Alpert's home and find the corpse of the shapeshifter... and no sign of the killer.
Later, Olivia meets with Peter and tells her how they've failed to find the killer. Peter suggests that they check Bolivia's laptop for further leads. Walter just stares at Peter. As Olivia goes, she tells Peter that he has nothing to be embarrassed about. Once she's gone, Walter explains that the Device is changing Peter, turning him into a living weapon. Peter asks what they do now, and Walter admits that he has no idea.
Brandon reports to Nina that they've found three copies of the First People's books. They are in three different languages, but all say the same thing. Further, Brandon's people have discovered that a few years ago, William Bell started a similar search.
At home, Peter looks at himself in the mirror.
At the research facility, the Device sits... and waits.