John McClennan looks at a photo of a young boy and then turns to Jeremy Roman, the young man he took it from. As he questions him about his memories and how he feels about them, he activates a chemical shunt that feeds a blue liquid into his victim’s brain. The victim continues to describe what he experienced until he dies, his tears freezing on his face.
In the lab, Walter runs around covering all the reflective surfaces while complaining about the shapeshfiters and their counterparts on the Other Side. Olivia arrives and is surprised to discover that Lincoln beat her there. Astrid figures that since Lincoln is new in town, he’s probably lonely, and hints that Olivia should date him. Olivia refuses, figuring that it would be awkward.
Broyles calls Olivia to the Federal Building and explains that 23 victims have been found, each one drilled through the skull and administered electrical current. What killed them was cerebral hypothermia because a coolant was administered to lower the brain’s temperature. When Olivia wonders why she hasn’t heard about the murders, Broyles tells her that they were committed on the Other Side and they’ve been asked to assist on the case. He asks Olivia if it’s going to be a problem.
Olivia and Broyles go to the hangar and meet with Fauxlivia. She explains that the killer finally left some DNA on his 23rd victim and they identified it as belonging to John Lewis McClennan, a man with no prior arrests. He has disappeared and Fauxlivia figures that he won’t get sloppy again. She wants them to bring John McClennan on This Side to the Other Side so he can provide some insight into their killer. They plan to take John to the murder sites and see what he can glean from the murder sites. Olivia talks to Broyles privately and registers her objections. Broyles figures that it’s difficult for her but she’s the only one he can trust to handle it. On This Side, McClennan teaches forensic psychology on serial killers, and they plan to take him over without revealing that he’s switched universes.
Olivia meets with John, who says he’s been working toward this type of case his entire life. She advises him that he’ll be tranquilized and taken to an unknown location. Agent Bergman comes in with a sedative and administers it to John.
On the Other Side, Fauxlivia dyes her hair blonde so she can pass as Olivia for the benefit of John. Olivia arrives and alt Lincoln thanks her and explains the surveillance setup. Agents bring in the sedated John.
Noreen Miller and her daughter Megan stop for gas and McClennan watches them from across the parking lot.
At Harvard on This Side, Walter listens to music in an effort to calm himself. Astrid arrives and tries to get his attention, finally turning off the music. She wonders what’s happening to him and Walter claims that his nerves are a bit raw. Astrid has checked his meds and confirmed that he’s overdoing it, and Walter admits that he’s been experimenting. When she asks if there’s anything specific going on, Walter simply says that he needs to rest and goes to his room to lie down.
John and Fauxlivia examine his counterpart’s house and he concludes that the killer is a self-taught genius and fascinated with the function of the brain. McClennan ordered parts from overseas for the schematics he designed but they have no idea what they were or what the killer did with them. Outside, Lincoln points out to Olivia that he can tell she’s nervous outside because Fauxlivia would be as well. Inside, John discovers that his alternate had chicken-hatching lights like the one he used at his father’s farm. He also finds jars of candy and figures that the killer was deprived and trying to make up for it without success. When John finds his counterpart's refrigerator and the food within, he concludes that the killer hunts for the day.
At the gas station, Megan goes to the restroom and McClennan gets up.
John and Fauxlivia go into McClennan’s den and John is surprised to see that the killer has the same old chair that he did. There is a photo of strangers on the wall and John explains that the killer is jealous of them because they’re happy, and he takes his victims when he’s happy.
Megan emerges from the restroom and discovers that her mother Noreen is gone.
John finds a photo of an older man standing by a tractor and tells Fauxlivia that the man is his father. He demands answers and Fauxlivia tries to calm him down. He storms out just as Olivia comes up to deal with him. He stares at the two Olivias in shock and then glances over and sees an amber containment zone down the street. Olivia takes John inside to explain while Fauxlivia blames herself. She wants to go in but Lincoln stops her.
Inside, Fauxlivia tries to explain about parallel universes and that some people have different lives because they make different choices. John explains that he’s known for some time that there was something different about him, a darkness, and that his father could sense it as well. As Fauxlivia comes in, John explains that his father tried to beat the darkness out of him and Olivia explains that she also came from an abusive home. John tells her that he became a forensic psychologist to help others. He considered doing what his counterpart is doing, but he found a woman, Margery, who helped him find small moments of peace to hold onto using love. As John admits that his life without Margery would have been like his counterparts, Lincoln calls Fauxlivia away. The professor then says that he’d like to tell his counterpart what he’s learned, but Olivia says that his counterpart can’t learn of John’s existence.
Lincoln tells Fauxlivia that Noreen has been abducted by McClennan an hour ago and the security cameras picked up McClennan. Olivia comes over and tells them that John wants to help. However, when they go inside, they realize that he’s left out the bathroom window and taken the photograph of his father with him.
At Fringe Division, Colonel Broyles isn’t interested in hearing their excuses and demands a report. Olivia explains that John plans to find the killer and stop him. Astrid analyzes John’s possible actions and warns that it will take up to 13 hours to track him. Broyles tells them to continue looking for John in the hope that he’ll find McClennan and Noreen. After the meeting, Olivia suggests to Fauxlivia that they trace the farm from the license plates on the tractor in the photo, the plates that she memorized.
McClennan shaves the back of Noreen’s head and then starts drilling. Before he can begin, John enters the room and the two men stare at each other in shock.
Fringe Division locates the McClennan farm and Lincoln tells his men to bring Noreen home unharmed. Fauxlivia invites Olivia to ride with him.
John tells McClennan that he doesn’t have to hurt him, and knows about the gun that his counterpart keeps hidden as he goes for it. He explains that he was like McClennan and was playing ring toss at a carnival on a night in October when his father found out about the dead things that he collected and came there to confront him. McClennan’s father took him home and beat him for three days, while John managed to get away. He made his way to a field and Margery found him. McClennan insists that he can’t stop the urges and no one can, but John says that he can and that he can show McClennan how to do the same. McClennan admits that maybe he can... and then knocks out his counterpart with a can.
As they drive, Fauxlivia and Olivia talk about their stepfather. Fauxlivia asks what happened to him and Olivia casually says that she killed him.
McClennan drills open the skull of his counterpart, inserts the electrodes, and feeds in the coolant. He then hooks the electrodes up to an outlet in his own skull and asks John to describe his happiest memories, including Margery.
The Fringe Division team breaks into the farmhouse and discovers that it’s empty, and realizes that they’re in the wrong place. Lincoln examines a nearby clearing and realizes that it contains the remains of the original farmhouse. They find a cellar door and go down.
John describes how Margery was kind and gentle. McClennan experiences the memories as John remembers how Margery treated him, even after she found the box where he kept his dead things. A few seconds later, Lincoln and Olivia come in. They find John unconscious on the floor. McClennan is in the next room, sobbing, and Olivia tells him to surrender. He wonders what he’s done and how he made the others suffer. John turns toward Olivia and shoots himself out of remorse.
Back on This Side, John is hospitalized and suffers from memory loss. Broyles informs Olivia that John has no memory of the last few weeks, and that the memories of Margery were extracted. They both wonder what will happen to John without the memories of Margery that changed his life. Olivia goes in to see him and confirms that John has no memory of her. She asks him if he remembers Margery and John says that he doesn’t. As she goes, John talks about how even when it’s the darkest, one can always step into the light. As Broyles and Olivia leaves, he admits that he’s always believed that some people can leave an indelible mark on other’s souls even if they don’t remember.
At the lab, Walter goes to bed and turns off the light. A voice calls out to him by name, asking if Walter can hear him and insisting that he’s right there. Walter insists that the voice is a fragment of his imagination and turns up his music as loud as he can. The voice begs him to help and Walter collapses, clutching at his head.