A Massive Dynamic team led by Nina and Dr. James Falcon is working on Walternate's machine. Nina tells Broyles, Olivia, and the Bishops that she heard they broke the encryption on the other Olivia's computer. Yes, Peter had some password ideas, and one, a song lyric, worked. "Fauxlivia ruined U2 for all of us," gripes Walter. That's what he's calling Bolivia now: Fauxlivia, as in Fake Olivia.
Anyway, everything's in one big file, Bolivia's mission details buried in hundreds of pages of observations about this world. They don't know what's valuable and can't discern any code.
The partially built machine is impressively big. But it doesn't have an energy source. Maybe that's the piece Bolivia stole, says Peter. Falcon asks if her files mentioned the machine. Suddenly, there's an electromagnetic spike. Monitors flicker as chairs and other items start moving. Then the machine shifts - and Peter's nose bleeds. When it stops, it exactly matches the Observer's drawing. What triggered it? Peter.
Late that night, Peter slips back into the house. When Walter comes in and says Peter's been out, he lies and says that he came downstairs because he couldn't sleep. Walter's obsessing over the First People book; it isn't showing him how the machine works or how it's connected to Peter. Peter says that Walter can't protect him from everything.
The next day at Massive Dynamic, Falcon preps Peter for an MRI over Walter's fretful, huffy protests. Every human has a unique electromagnetic signature, and they want to see if Peter's triggered the machine. In another room, Walter asks Nina for help in regrowing his missing brain parts. He wants William Bell's research on it. She reluctantly agrees.
Olivia visits Peter, saying that she called him last night but he didn't answer. He explains that he needed to take a walk. Hmm. During the scan, Falcon and Walter argue about Peter's high heart rate: 130 beats per minute. Falcon wants to do more tests. Walter is very against that.
Broyles asks Astrid to examine Bolivia's mission logs. But they're filled with personal observations, many regarding Peter. Astrid will be discreet. Then Broyles meets Olivia outside the Port Authority, where a shapeshifter's body was found. Michael Baird was killed around 3 a.m., and his data disk is gone. But why? Olivia thinks that Walternate sent a cleaner to kill Baird before anyone found out whatever he knew.
Astrid locates Baird's name in a long list of Port Authority employees. Broyles and Olivia wonder if someone on their side is a mole for Walternate. When Walter tells Peter this, Falcon overhears.
Everyone meets at Harvard, but Walter stays at Massive Dynamic, where they're questioning people who had access to Bolivia's hard drive. Astrid thinks that the file contains more shapeshifters' names, and Olivia wants to help, but Astrid balks. Peter realizes it's because Bolivia wrote about him. He and Olivia go to MD, where Brandon conducts interviews using Bell's special unbeatable lie detector.
Privately, Nina tells Walter that Bell designed a brain-regrowing serum using Walter's DNA. There are also rat and chimpanzee versions, and the labels on the vials were destroyed. She wants to diagnose them to determine which is Walter's. No time for that! Walter pops one open and snorts the contents.
Olivia tells Peter that she can handle reading Bolivia's file. Peter's worried that Bolivia thought he was a fool, and he doesn't want Olivia seeing that. Brandon calls Falcon in for questioning, but the doctor left early. Because he's a shapeshifter. Who's already dead when Broyles, Olivia, Peter, and an FBI team raid his house. Astrid finds Falcon's name in Bolivia's list of Massive Dynamic employees.
Falcon's body goes to Walter, who suddenly craves a banana and makes a chimp-like gesture of dominance. Oops, wrong serum!
Olivia apologizes to Peter for thinking only of her own pain and not about what Bolivia did to him. But they can get past this. Peter smiles. He says that it's time for more tests at MD and asks her to tell Walter he'll be home late.
Elsewhere, someone pursues a shapeshifter. She kills a panhandler and changes into him but still gets killed - by Peter!
When Nina phones the Bishops' house to schedule more tests with Peter, Walter realizes that Peter lied to Olivia. He finds pages from Fauxlivia's file in Peter's room, with Baird's and Falcon's names circled.
Olivia insists on helping Astrid. She reads something Bolivia wrote about Peter and realizes that she was falling for him. She would see what I see, says Olivia. This sparks an idea. Both Olivias' moms called them "Olive" as children. This word forms a code, and they find the other shapeshifters.
The final shapeshifter fights Peter off, but Walter bursts in and startles it. Peter shoots it, then tells a stunned Walter that he hasn't learned anything from the others' disks, but maybe this time he will. He's tired of just reacting. Walter asks if this is what the old Peter was like, manipulating people who care about him? Peter says the shapeshifters aren't human, so he's not doing anything wrong. Walter quietly asks then why didn't he tell them?
Back at home, Walter says that every relationship is reciprocal: When you touch something, it touches you. When Peter touched the machine, it changed him. Peter asks, what now? Walter doesn't know.
Brandon shows Nina three copies of the First People book they've found. They've also learned that, a few years ago, somebody started a similar search: William Bell.
Olivia reads Bolivia's journal at home, while Peter stares out his window. Elsewhere, the machine sits, glowing faintly. Waiting.