After her disappearance, Peter and Lincoln go to Olivia’s apartment to search for clues. Lincoln thinks that Nina is responsible, but Peter warns that she won’t be easy to confess. The discuss Walter’s theory that Olivia has been acting strangely due to the cortexiphan that she’s been dosed with, and Lincoln realize that Peter may have been superimposing his memories of his Olivia on their Olivia. Peter is more interested in searching the apartment, and finds a hidden camera with a 6-hour memory chip in the security alarm. He says that he may be able to access the information and goes to Harvard to meet with Walter.
Nina and Olivia, locked up in an abandoned hospital room, discuss their situation. Nina says that she’s been a prisoner for weeks, ever since her doppelganger abducted her. David Robert Jones comes in with his assistant, Leland Spivey, and welcomes Olivia. She explains that she already knows him because she has the memories of her counterpart from Peter’s timelines, including the ones where she saw Jones die. When she wonders what she’s been doing to him, Jones explains that he’s been giving her cortexiphan, but that he’s not the one who started the procedure. He’s aware from Walter’s notes that extreme emotion can activate her abilities, and then uses a hand drill to torture Nina by boring into her cybernetic arm.
In Boston, four of the Observers meet in a public square. They wonder where September is and why he hasn’t eliminated Peter from the timeline. The nominal leader, November, says that they’ll wait until September resurfaces and then make him face the consequences of his actions.
Broyles interrogates Nina, who insists she had nothing to do with Olivia’s disappearance. Lincoln arrives with a file showing the biometric readings from the Massive Dynamic deep-confinement vault. Despite her denials, the records show that she was in the vault with the cortexiphan several times. Nina insists that a shapeshifter must be responsible, but realizes that they don’t believe her and demands to have a lawyer present before she answers any more questions.
At Harvard, Peter and Walter are examining the camera’s memory chip and explaining to Astrid how they may be able to recover the erased images from the camera’s previous recordings. As they work, Walter blames Peter for endangering Olivia by first transposing his memories onto her and then taking her out of the lab. Peter manages to find some of the copied-over images and starts trying to clarify them.
Jones and Leland come back to the room and remove Nina. Jones then brings out the light box and tells Olivia that he plans to use Nina to trigger Olivia’s abilities. He opens a shutter into the next room where Olivia has been wired to a car battery. As Leland prepares to torture her, Jones insists that Olivia’s potential is far greater than simply lighting up bulbs. She tries to light the bulbs with her mind but nothing happens and Jones orders Leland to begin the electro shocks. After a few minutes, Olivia says that she needs to rest and Jones gives her an hour to recover before they start again.
Peter manages to resolve the image of the person who planted the camera in Olivia’s apartment and Astrid sends it to Fringe Division. As Peter speculates that Jones is trying to activate Olivia’s abilities just like he did in Peter’s timeline, the Observer September appears in the lab, bleeding from the chest. He says that Peter is right and Olivia needs him, and then collapses. Walter examines September and Peter assures him that the Observer is essentially human. While Walter tends to September’s collapsed lung, Lincoln calls to say that they have the image that Astrid sent and that Nina’s lawyer has gotten her released.
Nina is returned to Olivia’s cell and her adoptive daughter asks her to help trigger her abilities. However, Olivia admits that her memories of her own life are fuzzy. She asks Nina go over her life and Nina describes how she picked up Rachel and Olivia at the hospital, and that Olivia insisted on calling her “Mrs. Sharp.” The first night that Olivia slept at Nina’s house, Nina was finally able to convince her to call her Nina. Olivia starts to remember but admits that it isn’t enough and that only Peter’s presence has been able to let her access her powers. Nina suddenly clutches at her chest in agony and Olivia calls for help. When Leland comes to investigate, Olivia warns him that if Nina dies then Jones loses his only leverage over her. Leland gives in and has his men move Nina out. As soon as they’re down the hallway, “Olivia” stops feigning illness and tells Jones that they need Peter.
Broyles comes to the lab and tells them about Olivia meeting September at the opera house and his telling her that she has to die in every timeline. Walter speculates that since the Observers exist in all times simultaneously, that September is at the opera house several months ago and here at the same time. Astrid returns with information on Leland, the man who planted the camera in Olivia’s apartment. According to the files, he died in a car accident three years ago. Peter figures that it’s dead end and says that he has an idea, and Walter realizes that he plans to use the brainwave-merging equipment to enter September’s mind and learn what they need to know. Walter advises against it, noting that if September dies while Peter is in his mind then Peter could die as will. Despite the risks, Peter insists and Walter admits that he can do it.
Walter begins the procedure and Peter finds himself in a glass chamber looking out on the creation of the universe. September appears and says that he knows that he has been shot and is dying. However, he insists that neither his shooter nor Olivia’s location is important. He explains that he and the other Observers are scientists from one of humanity’s possible futures. They travel back in time using their technology to observe their beginnings, but Peter notes that they’ve done more than observe. September admits that he’s had to rectify the mistake that he made in the past, and shows Peter the moment when he went to see Walter in his lab and distracted him from finding the cure for Peter as a child.
Back in the observation room, September explains that he couldn’t let Peter drown at Reiden Lake because of his importance. He shows Peter images of the timeline that was and would be, when Peter has a son named Henry, born of Olivia. However, since Henry wasn’t born with the original Olivia, the timelime was altered. Peter entered the Machine and erased both himself and Henry, but somehow Peter has returned in physical form despite September’s efforts. The Observer now believes that Peter has to exist to put things right and have a child by “his” Olivia. The mindscape starts to waver and September warns that “they” are coming and there’s something that Peter has to do. Peter asks the Observer where he can find Olivia, but September simply tells him to go home.
Peter wakes up at the lab as the Observer’s condition worsens. September convulses... and then disappears. Peter tells the others what September said, and Lincoln wonders how it’s possible when Peter has been insisting that the two Olivia are the same. Broyles and Lincoln leave to interrogate Nina before she can be released, while Walter tries to assure Peter that he did what he could. Peter decides that September was being literal and wanted him to go to his home to find Olivia. Astrid isn’t convinced of the logic but Walter says that it makes as much sense as anything. When Peter arrives home, he finds Leland waiting for him, and the intruder has his men knock Peter out and haul him away.
Back at the abandoned hospital, Olivia is waiting when Leland opens the shutter to reveal Peter in the adjoining room with Olivia. Jones comes in and tells Olivia that Leland will start cutting Peter if she doesn’t demonstrate her abilities. Peter tries to stop her but Olivia agrees and concentrates. The light box lights come on almost instantly and Jones congratulates her, but the overhead lights start to flicker. When Jones wonders what she’s doing, Olivia explains that she feigned her earlier amnesia to get “Nina” to slip up and make a mistake: Olivia didn’t call Nina “Nina” until her high school graduation. Jones escapes with Nina as electricity arcs down from the lights and electrocutes Leland. Olivia frees Peter and they go after Jones and the shapeshifter. Olivia starts to weaken while one of Jones’ men comes after them. Peter manages to hold him off long enough for Olivia to shoot him.
Jones and Nina activate the bridge to the Other Side just as Peter and Olivia arrive. The fake Nina goes through while Jones congratulates Olivia for the strength of her love for Peter. He turns to walk through the bridge and Olivia shoots him in the throat. Smiling, Jones says that his body was reassembled at the atomic level, making his skin much tougher. He goes through the portal and closes it, and Peter leads them out of the hospital.
As Peter calls for help, Olivia starts to recover. He worries that his memories combined with her abilities are altering her memories like Walter said, and admits that at the gas station he was ready to accept her offer. Peter insists that it would have been a mistake and that he saw the Olivia that he is fated to be with. Olivia insists that she is Peter’s Olivia, but he tells her that he’s only seeing her for what he wants to see, and says that Walter will find a way to undo the false memories. As Olivia begs him to stay, Peter turns and walks away, saying that it’s better that he keep away from her and that he’s going home.