John McClennan interrogates Jeremy Roman, a man that he's strapped into a chair. As McClennan tells Jeremy to talk about his childhood, he pumps coolant into Jeremy's brain through a hole that he has drilled in the back of his skull. Jeremy keeps talking about his childhood until he dies, a tear freezing on his face.
In the lab, Walter is covering up the reflective surfaces and telling Lincoln about the shapeshifters on the Other Side. As he starts complaining about Walternate and his people, Astrid arrives and reminds him that they agreed to forget the past and move forward. Olivia comes in Astrid suggests that she might date Lincoln. However, Olivia refuses, saying that they'd end up breaking up and things would be awkward.
Broyles calls Olivia to headquarters and explains that McClennan has killed 23 people, drilling into their skulls and rigging up electrodes, and then injecting coolant so that they froze from the inside. When Olivia notes that she hasn't heard of the murders, Broyles explains that the murders were committed on the Other Side, and they've been asked to assist their counterparts.
Olivia and Broyles go to the hangar and Bolivia crosses over to meet with them. She explains that the killer finally got careless and left his DNA on the 23rd victim, and they confirmed he was John McClennan. McClennan has disappeared and Bolivia figures that he won't make another mistake. The Other Side Fringe Division wants Olivia to bring McClennan's counterpart John to their side so he can examine his counterpart's home and provide them with any insights. Bolivia objects to the idea and Olivia isn't thrilled about it, but Colonel Broyles has overridden Bolivia. Olivia talks to Broyles privately and he tells her that they're going to do it. When Olivia wonders how they'll pull it off, Broyles explains that their John McClennan is a forensics psychology professor who specializes in serial killers, and they'll take him over without revealing that he's been transferred or who he's examining.
Olivia meets with John at his office and he agrees to help. He tells her that he's been hoping to take on this case his entire life. Olivia tells him that they're trying to keep the case out of the news and that they'll sedate him and take him to the house in Norristown, PA. John agrees and Agent Bergman comes in to give him a sedative.
On the Other Side, Bolivia dyes her hair blonde to pass as Olivia. Lincoln admits that it looks good on her. Olivia arrives with the sedated John and Lincoln thanks her for his help. They take John inside and have Olivia monitor the conversation from a nearby surveillance van.
Noreen Miller stops at a gas station with her daughter Megan. As Megan cleans the windshield, McClennan watches her from across the street and drinks coffee.
At Harvard, Walter listens to music to calm himself. Astrid comes in and has to turn off the music to get through to him. He claims that he is simply jumpy but Astrid figures that something else is going on and asks for the truth. Walter simply says that he needs to rest and walks away.
John examines McClennan's home and accurately profiles his personality. Bolivia informs him that McClennan ordered parts from overseas for his schematics, but they have no idea what he used them for. As John talks, Olivia listens in and Lincoln figures she's hate being out of the action because Bolivia would react the same way. Meanwhile, John finds egg-hatching lights and notes that his father worked on a farm and they had chickens. He concludes that the killer grew up deprived and is deeply unhappy, and that he hunts during the day and tries to blend in.
At the gas station, Megan goes to the bathroom while her mother finishes filling up their SUV.
John examines McClennan's den and recognizes his chair as the same one he had in his own home when he grew up. They find photos of dozens of strangers taped to the wall, and John says that the killer hates happy people and takes them when they're at their happiest so he can make himself happy.
Megan comes back to her mother only to discover that she has disappeared.
John looks at the photos and finds one of an older man standing in front of a tractor. He realizes that the man is his own father and starts to panic. Olivia leaves the van to help him as John storms out. He comes to face with a second Olivia, and then looks to his left and sees a mass of quarantine amber. Olivia takes John inside while Lincoln holds Bolivia back so his partner can deal with John. Inside, Olivia explains the concept of parallel universes and people making different choices. John admits that he has the same feelings as his counterpart, the same darkness, and his father tried to beat him out of it. As Bolivia comes in, Olivia admits that her stepfather was also abusive. John says that he learned forensic psychology to help other people like himself, and he learned to control the darkness after he met a woman named Margery. Without her, John imagines his life would be like his counterpart's. Lincoln calls Bolivia away and Olivia warns John that McClennan can never know that John exists.
As Olivia comes out, Lincoln informs his partner that security cameras picked up McClennan abducting Noreen at the gas station. They go back into the house and discover that John has left and took the photo of his father with him.
The team goes to Fringe Division and reports to Colonel Broyles. Lt. Farnsworth tries to calculate where John would go given his unfamiliarity with the Other Side. It will take her 13 years to follow her, but Olivia suggests that they find where McClennan is holed up using the license plate on the tractor in the photo.
McClennan prepares to drill into Noreen's skull, but John arrives and interrupts.
Fringe Division locates the farm and Lincoln sends his men in with orders to make sure they get Noreen out unharmed. As they leave, Bolivia invites Olivia to come with them.
John tells his counterpart that he's safe, and knows where he hides his gun. He tells McClennan that when he was a child, he went to a carnival on an October night and was playing ring toss when his father came to get him and beat the darkness out of him for the first time when he found the dead things. While the father dragged McClennan home and beat him, John managed to escape and made his way to a field where Margery found him and took him in. Now John can control the pain, and he offers to show McClennan how to do so as well. McClennan admits that he might, but then knocks John out.
As they drive to the farm, Bolivia asks Olivia what happened to her stepfather, Olivia casually says that she killed him.
McClennan inserts the electrodes into John's skull and starts pumping in coolant fluid. He hooks the other end of the electrodes up to an outlet in his own skull and then asks John to talk about his happy memories of Margery.
Lincoln and his men search the farmhouse but find no signs of McClennan or John. However, Lincoln realizes that the ruins of the original house are nearby and finds a cellar door.
John talks about his time with Margery and McClennan realizes the emotions via the electrodes. The killer smiles at the shared memories of how Margery accepted John even knowing he killed small animals. Lincoln and Olivia break into the cellar seconds later and find John and Noreen, still alive. Olivia searches the next room and finds McClennan, crying at the memories and what he's done to all his victims. He then kills himself in remorse before Olivia can stop him.
Olivia takes John back to this Side, where they confirm that he will confirm but he'll have no memory of the last few months. He has also lost his memories of Margery, and Olivia worries that without those memories John may become a serial killer. She goes to see him and confirms that John has no memory of her. She thanks him for helping to save one woman and many future victims, and asks if he remembers Margery. John has no knowledge of her and admits that things are dark for him. As Olivia goes, John notes that even when it's the darkest, someone can step into the light. As they leave, Olivia believes that John still remembers what Margery taught him and Broyles admits his belief that there are people who leave an indelible mark on other persons' souls.
In the lab, Walter prepares for bed and turns off the light. Peter's voice calls out his name from nowhere, but Walter dismisses it as a figment of his imagination and tries to drown out the voice by turning on the music as loud as he can.