Grant Russo is at a train station about to board a train. As he passes near a well-dressed Gentleman carrying a folded umbrella, he is "accidentally" poked with the umbrella.
Russo goes to his home in Rye, New York, unaware that the Gentleman has followed him home. Russo grows steadily weaker as he goes inside, and finally collapses. When he wakes up, he finds himself strapped to an operating table, covered in blood. The gentleman is calling 911 for medical help. Once he finishes the call, the Gentleman apologizes to Russo and says there's no other way, and then injects something into his neck. Russo convulses and then passes out.
The EMTs arrive at the house and go inside, and discover plastic blood-covered sheets hanging from the ceiling. They find Russo inside, his chest pried open and his heart removed Russo comes to life and begs them not to let him die.
The Gentleman goes back to the train station, carrying a cooler, and waits.
Broyles returns to his office and finds Olivia there. She explains that Walternate is driven to destroy their world to save his. When Olivia insists on investigating, Broyles informs her that she's going on a leave of absence. Olivia feels that she would be better off working on the case, and says that she made a promise to a friend to do everything possible to save both worlds. Realizing she's talking about his counterpart, Broyles asks her about his other self, and she explains that the alternate Colonel Broyles was an honorable man, and was happily married with a wife and two children.
Peter leaves with Walter to meet Olivia at the crime scene, and Walter wants to talk about how Peter was involved with Bolivia. Peter reluctantly admits that he's going to tell Olivia what happened, even though he fears it'll change their relationship permanently. His father says that Peter is a good man, and that Olivia knows that. They meet Olivia and Broyles, and Broyles assures them that Olivia has been approved for duty. He then tells them what happened, and that Russo lived for three minutes after the EMTs found him without his heart. Impressed, Walter checks out the body and thinks it looks similar to a Scandinavian method of torture. The incisions are precise, and there's scar tissue indicating that the victim had heart surgery before. Peter gets an idea and checks Russo's medical cabinet. Meanwhile, Walter demonstrates that the corpse still has reflexes, and that he can't determine for sure if the man is dead. Peter shows them all of the drugs the man has, that were prescribed by a Dr. Alexandra Ross.
Peter and Olivia go to the hospital to see Dr. Ross. While they wait for her to get out of surgery, Olivia talks about how odd it feels to come back and discover someone else has been living her life. Peter explains how he noticed differences between Olivia and her counterpart, but he dismissed them. Olivia says that it's okay, and Peter then tells her that he thought Bolivia was her, and he had a relationship with her. Olivia confirms that everyone knows once he had to report it after they discovered Bolivia was the imposter. She then admits that that her counterpart had a full life, and that things might have been different if Bolivia's boyfriend had been in town. They get word that Dr. Ross is out of surgery, and Olivia assures Peter that it's okay.
Peter and Olivia ask Ross about the medications, and he explains that Russo wanted a second chance and was on the standard regimen for heart transplant recipients.
In a basement lab, the Gentleman is playing cal music while stitching together a young woman's corpse. He assures her that he'll soon be finished.
At Harvard, Walter is examining Russo's corpse while having Astrid checking the files on the Yatsko project, a program that he and Bell worked on to interrogate corpses after they were dead. As Astrid leaves for the night, Peter arrives and Walter asks him to smell Russo's corpse. The corpse isn't decomposing, and Walter explains that he and Astrid isolated a serum that is slowing down the petrification. He believes that the organ thief tried to preserve his victim's life, and that Russo could have been saved if the EMTs had put him on a heart-lung machine. Walter then asks if Peter told Olivia, and is surprised to learn that she reacted well.
As Olivia gets dressed in her apartment, she examines the tattoo that Walternate had put on her neck to convince her that she was Bolivia. She then goes through her closet and throws all of the clothing on the floor. Olivia then yanks the sheets off the bed and takes them to the washer, and finds more clothes inside. Crying, she crouches on the floor.
The next morning, Olivia arrives at the Federal Building and Astrid asks how she's doing, being back. Olivia tells Astrid what Peter told her, and asks Astrid what Peter was like with Bolivia. Astrid says that the feelings Peter had for Olivia's counterpart were for her, and they are still there.
Broyles briefs Peter and Olivia on the discovery of a number of similar organ thefts. All of the victims were organ transplants, and had received donations from the same anonymous female donor. Her corneas were donated to the Rosindale Eye Bank, and Broyles calls to find out who received them.
The Gentleman is working on a man, Ben Killenberg, preparing to remove his corneas.
Astrid gets the name of the donor, Amanda Walsh, and calls Broyles. He, Olivia, and Peter are at the restaurant of the man who received the corneas. They find indication that surgery recently took place on a table in the kitchen, and hear a noise from the walk-in freezer. Investigating, Olivia finds the restaurant owner… his eyes missing.
At the hospital, Peter and Olivia talk to the victim, who explains that he collapsed and woke up to find himself in the middle of surgery. He says that the Gentleman apologized to him, but insisted that the corneas didn't belong to him. They leave to talk to Amanda's family.
At the lab, Walter is working with the serum and considering the possibilities of a substance that prevents the decay of milk and cheese. Astrid brings in the Yatsko Project files, which show that the work continued after Walter was committed. Walter says that they need to find Amanda's body.
Peter and Olivia talk to Amanda's mother, who explains that the only thing that interested Amanda was ballet. Amanda suffered from clinical depression, participated in group therapy, and eventually killed herself. As Olivia's gets the names of the doctors Amanda met with, Astrid calls and tells Peter what Walter wants. He goes back inside and asks Mrs. Walsh for permission to exhume Amanda's body. She refuses, explaining that it was cremated.
Peter takes the ashes to the lab, and Walter tastes the ashes. He then tells Astrid and Peter that it's wood ash, not human remains. He figures Amanda's body is with her organs, and concludes that the person who is stealing the organs is trying to put Amanda back together again.
In his lab, the Gentleman rigs Amanda's body in an elaborate series of straps and mountings. He then turns on some music and uses a series of levers and pulleys to manipulate Amanda's corpse into dancing.
While Walter works on Russo's corpse, Astrid gets a call from Broyles. He's confirmed that Amanda's corpse was stolen, and the funeral home covered it up. Walter explains that he and Bell dabbled in the resurrection of the dead when they tried to bring back Peter's cocker spaniel.
Peter and Olivia go through Amanda's medical files, and Peter notes someone who worked as hard as Amanda to overcome her depression should have gotten some results. Olivia dismisses Peter's suspects, insisting that he's not properly profiling. She says that whoever is bringing Amanda back loves her, and Peter's suspects don't. Olivia snaps at Peter, who says that it's okay. Peter comes up with the name of Roland David Barrett, who dropped out of group therapy the day that Amanda committed suicide. As they drive to Roland's house, Peter confirms that the man was working on the prevention of cell decay, and wonders if he found a way to resurrect the dead.
In his basement lab, Roland applies electrical shock to Amanda. She finally breathes and comes back to life, staring wildly around her. Roland tells her that she's back, and that he kept his promise to be there for her, just as she promised to be there for him. He gets her to calm down, but realizes that she's not displaying any cognitive function. The FBI team bangs on the door and prepare to break in, and Roland runs out.
The Fringe team enters the house with the FBI, and hears Roland moving upstairs. When they go to investigate, Roland tries to slip out but Olivia captures him. He tells them that Amanda is downstairs. As the others check out the basement, Roland tells Olivia that he was trying to give Amanda another chance after she made a mistake. However, when he brought her back, he looked into her eyes and realized that whatever he brought back, it wasn't Amanda.
Walter examines Amanda's body and confirms that it's dead.
As the FBI cleans up, Peter finds Olivia sitting in the back, crying. She tells Peter what Roland said about realizing that Amanda wasn't real, and tells Peter that she held on to the image of him through everything she went through on the Other Side. Olivia wonders why Peter couldn't do the same, and says that she can't handle going back to the life that her counterpart took from her... including Peter. She walks away, leaving Peter sitting alone. Once she's left, he says that he's sorry.
Later, the Observer watches as Peter takes Walter to an ice cream shop. He calls someone and says that he's arrived, and that the one they're interested in is still alive.