The Fringe team arrives at the Massive Dynamic base where the Machine is being kept. As they show their IDs, Walter asks for chewing gum to deal with the pressure in his ears. Once inside, they find Dr. James Falcon explaining that they haven't been able to activate the Machine. Nina meets with the team, and Broyles explains that Peter was able to break the encryption on "Fauxlivia”'s laptop computer. However, there is too many of her personal observations to make it easy to find the relevant data on the Other Side's plans. Falcon tells them that with all of the resources at their disposal, they're unable to decipher the Machine's function. Walter realizes that Falcon works for him and introduces himself. Meanwhile, the scientists discover that the Machine is giving off an electromagnetic spike, disrupting electrical equipment and magnetizing iron objects. As the team realizes that Fauxlivia has a critical part, Peter discovers that his nose is bleeding. They look up as the Machine activates itself, and Peter tells them that he triggered it.
Late at night, Peter returns home and tries to make sure that Walter doesn't hear him. As he goes to the kitchen to make himself a sandwich, Walter comes down and Peter claims that he was sleeping and decided to come downstairs. He says he's fine, and Walter notes that he was reading over the book on the First People. There's nothing saying how the Machine is connected to Peter. Peter tells him to stop, and says that this time there's nothing Walter can do for him.
The next day, Peter goes to Massive Dynamic so Falcon can test him for electromagnetic readings. Walter insists the tests aren't necessary, and warns Peter that he's exposing himself to dangerous levels of radiation. Once they're alone, Walter argues for firing Falcon, a gifted bio-medical engineer, but Nina refuses. Walter admits that he's terrified for Peter. Next, he asks Nina to find the detailed research notes that William Bell left on the operation he performed on Walter's brain, so that Walter can be smart enough to figure out Peter's connection to the machine. Nina agrees to help.
Olivia comes to see Peter and notes that he didn't take her call last night. Peter claims that he went for a walk to take a break from Walter. Falcon puts Peter in the scanning chamber and begins the tests.
At the Massachusetts Port Authority, a man goes outside to the koi pond for a smoke. He notices dead fish in the water and a silvery substance. When he brushes aside the water lilies, he finds a dead man with a bullet hole in his forehead.
Broyles comes to see Astrid at the lab and explains that he wants her to examine Fauxlivia's data. However, he asks her to keep the information concerning Fauxlivia's involvement with Peter discrete. As she agrees, Broyles gets a call about the dead man.
Falcon has detected a slight heart-rate increase, and Walter demands that they remove Peter. The doctor refuses and Olivia tries to mediate. Broyles calls to summon her to the Port Authority. He explains that the fish died of mercury poisoning after the shapeshifter, posing as Michael Baird, was shot, and the data storage unit in his back was removed. They soon conclude that Walternate sent someone to assassinate the remaining Shapeshifters on This Side. Broyles realizes what that means and calls Astrid, and tells her to check the data file for information on Michael Baird. When she tells Broyles that Baird is on a list of Port Authority employees, Broyles tells Astrid to shut down all access to the datafile. He then explains to Olivia that Astrid cracked Fauxlivia's list 36 hours ago, and someone must have known she did it: someone within the organization.
When the tests are done, Falcon tells Peter that he proved and they can't find anything that would have activated the Machine. Walter comes in to tell his son that they've found a dead shapeshifter, and they have a traitor in their organization. Peter thanks Falcon and leaves for the Harvard lab. Broyles insists they've rounded up everyone who could be the mole and checking for any recent changes in behavior Olivia offers to help sort the data, and Astrid objects. Peter realizes that much of Fauxlivia's files are like a diary, and Peter is prominent. Peter heads to Massive Dynamic to join with his father, who is testing the suspects at Massive Dynamic.
At Massive Dynamic, Brandon checks the next suspect, while Nina and Walter monitor his questioning using a sophisticated lie detector created by William Bell. The blood tests are negative, but don't rule out human moles. Peter insists they keep all the suspects in custody, and snaps at Nina when she objects. Nina then talks to Walter in private and gives him Bell's research. There are three retrovirus vials, and the labels were burned off in a lab fire years ago. The right vial will regrow Walter's missing brain sections. However, the other two samples are for a rat and a monkey. Nina wants to run lab tests before proceeding, but Walter immediately sniffs one of the vials. Nina suggests that Peter talk to a psychologist, but Walter insists that he's the one who needs to help his son.
As Olivia and Peter watch the next interrogation, Olivia says that she won't be upset by reading about Fauxlivia's sexual encounters. However, Peter says that he knows what Fauxlivia would have said about him as the target of her con, and he doesn't want Olivia to see him like that. Brandon informs them that everyone has tasted negative, but Olivia suggests that they test Falcon. They try to call him in and discover that Falcon has left early for the day.
Olivia and Broyles take a FBI team to Falcon's house and find his dead body, leaking mercury from two head wounds. They call Astrid, who confirms that Falcon is in one of Fauxlivia's lists. Meanwhile, Walter gives himself an IQ test and realizes that he's showing no sign of improvement. Once she hangs up, Olivia complains that they're always one step behind, and they need to find one live shapeshifter.
In the lab, Walter prepares to dissect the Falcon shapeshifter, but has a sudden craving for bananas, which he hates. As they dissect a body, Walter asks what Fauxlivia wrote about him. Astrid tells him that the infiltrator thought he was kind and brilliant. As they examine the Falcon shapeshifter's corpse, Walter snarls and realizes that he's displaying dominance. He realizes that he must have sampled the retrovirus for the chimpanzee, but assures Astrid that his immune system will soon reject it. As they check the corpse, Walter finds blood beneath the shapeshifter's fingernails.
Olivia examines the window and realizes that the killer broke in through the window, indicating that Falcon didn't know him. She then apologizes to Peter, saying that she was so focused on what Fauxlivia did to her that she didn't think of what she did to Peter. However, Olivia says that now Fauxlivia is gone and they can get past it. Peter smiles and thanks her, and gets a page from Massive Dynamic saying he's due for more tests. He asks her to tell Walter not to worry and leaves. Astrid calls to tell Olivia that they've confirmed that the Falcon shapeshifter's attacker was A Positive, and Walter notes that he has that blood type, along with a third of the population. However, there is only one person with that blood type who had access to Fauxlivia's files: Brandon
On the streets, a shapeshifter in female form, Jackie Bermudez, runs through the streets into an alleyway. A transient asks her for change, and she breaks his neck and then uses the duplication Machine to take on his form.
Broyles and Olivia confront Brandon, who is eating his lunch. He apparently has no idea why they believe he's a shapeshifter.
The shapeshifter finishes its transformation but a man steps out of an alleyway and shoots it dead. It's Peter.
Brandon undergoes questioning via the lie detection and passes. Olivia returns to the lab and tells Astrid that she's going to help. She insists that the future is what matters, not the past, and they're running out of options. Olivia believes that she can anticipate her alternate's thought patterns and find something that Astrid hasn't.
Walter is at home making a banana split when Nina calls him. He tells her that he knows what the first sample is, but she says that she was calling Peter to schedule a new round of test. Remembering what Olivia told him, that Peter was going in for testing, Walter realizes that something is wrong. He says nothing to Nina, but goes up to Peter's room. Among the papers is the list of suspects from Fauxlivia's data file. Several of the names are circled.
Peter is watching the apartment of the remaining shapeshifter, who returns home from shopping.
Reading Fauxlivia's files, Olivia discovers that her counterpart had real feelings for Peter. She realize that they use the same language, and concludes that Fauxlivia used her mother's nickname, Olive, as the basis for a substitution code. The names corresponding to the letter positions are the dead shapeshifters they've discovered to date, and the last one is Zach Alpert.
Peter breaks into the Alpert apartment and shoots the shapeshifter as he watches TV. However, Peter discovers that it's a dummy. The shapeshifter attacks and disarms him, and then demands to know where Peter is getting his information. When Peter refuses to talk, the shapeshifter says that he's not allowed to kill him, but he can torture him. Walter comes in and Peter takes advantages of the shapeshifter’s distraction to knock him into a chair. He grabs a cleaver, cuts off the shapeshifter's fingers as he reaches for a gun and then shoots him.
Olivia calls Broyles to tell her what they've discovered, and they both head for Alpert's apartment.
Walter explains that he saw the names and looked Alpert up in the phone book. As Peter cuts open the shapeshifter's data storage slot, Walter realizes that his son killed the other shapeshifters. Peter insists that he can no longer be reactive, and that the shapeshifters he killed are soldiers. he insists that he's not doing anything wrong and then kills the shapeshifter. Walter asks why he didn't tell them if he thought he wasn't doing anything wrong, and insists that Peter isn't himself. Olivia calls Peter and tells him that she's on the way to Alpert's apartment. She and Broyles arrive a few minutes later, but only find the shapeshifter's corpse.
Later, Olivia comes to see Peter and Walter. She says that they've lost their only lead, but Peter suggests they continue to examine Fauxlivia's laptop computer. As she leaves, Olivia tells Peter that she read Fauxlivia's file and he has nothing to be embarrassed about. Once she leaves, Walter tells his son that the Machine is changing him, turning him into a weapon. Neither one of them know what to do next.
Brandon tells Nina that they've located three copies of the First People's book. They're in three different languages and written by three different authors, but they're word-for-word identical. Brandon admits that it's possible that sometimes in the last six major extinction events, a great civilization may have been wiped out. He also tells Nina one other thing: they've discovered that Bell was looking for the books a few years ago.
At home, Peter stares at himself in the mirror.
In the Massive Dynamic facility, the Machine sits... and waits.