After she kisses him, Peter asks why Olivia did so. She insists that she’s fine and says that they kiss, and it feels normal to her. When Peter questions her, Olivia admits that she’s only known him for three months. She suggests that it might be a residual effect of the events in Westfield and says that she needs some rest. Peter offers to stay the night but Olivia says that she wants some time alone and that she is getting a migraine. Peter agrees in return for her word that she’ll see Walter if she feels the same way in the morning.
At the Deerfield Mental Hospital, Sean Keenan wanders through the hallways and listens to a voice in his head saying that it’s time.
In Douglaston, New York, three home intruders break into a house belonging to a reporter named Daniel Greene. Meanwhile, the hospital supervisor, Bernadette, finds Sean and takes him back to his room. As they go, he continues to hear the voices of the intruders and insists that they’re real.
The three intruders close in on Green and one of them slams him through a mirror. At the hospital, Sean screams in pain as one of the attackers cuts himself on the glass. The three killers finally suffocate Greene with a plastic bag. Bernadette and an orderly give Sean a sedative, but he suddenly snaps out of his cell and says that Greene is dead.
The next day, the Fringe team gets word of the incident when a nurse hears about Greene’s death on a newscast and remembers that Sean described the same murder. Olivia, Lincoln, Walter, and Astrid go to the hospital and talk to Bernadette. She explains that Sean is a self-admitted patient and has spent three years at the hospital and years previous to that at other institutions. However, this is the first time he has had such a vivid experience. As they go to see Sean, Olivia suddenly has a memory of flash of going to St. Claire’s with Peter, even though Peter isn’t with her at Deerfield.
The agents interview Sean, who doesn’t recognize Greene. The young man explains that the voices in his head killed Greene, but he doesn’t hear them now. Walter asks him about the voices and Sean says that he heard two of them say that they were going to the train station while the third killer went into the bathroom to wash up. While Lincoln calls the authorities to start a search, Sean explains that the voices never talk to him but only to each other. Walter suggests that Sean go off his medications for schizophrenia so that they can explore the voices further.
As Bernadette gives her files to Olivia and Astrid, Walter accuses her of misdiagnosing Sean. He explains that the voices in Sean’s head are caused through telepathy, not schizophrenia, because they don’t talk to him. Olivia explains about their plan to take Sean off his meds and agrees to go with Bernadette and explain to Sean's physician. As she walks down the hall, Olivia has another memory-flash of walking down the halls of St. Claire to get Walter out.
That night, Olivia comes to see Peter at his home, the one he also has in his timeline. She recognizes the thing in the house and talks about how after the merger at the apartment building, she and Peter returned to the house and made love for the first time. Olivia tells Peter that she remembers everything that “his” Olivia did in his timeline, up to and including the point where he entered the Machine and sacrificed himself to save both universes.
The next morning, Walter gives Olivia a full exam despite her insistence that she feels fine. It turns out that she can still has her own memories of her timeline, but that they seem like a dream to her. Walter speculates that the cortexiphan trials gave her an enhanced empathy and she’s drawing on Peter’s memories to make him happy. Peter insists that he isn’t willingly doing anything, but Walter isn’t convinced. Walter takes a few strands of Olivia’s hair to test, while Lincoln arrives to report that the authorities found bloody paper towels right where Sean said they would be found. A DNA test shows a strand that is similar to one that Walter recognizes from Sean’s report. He confirms that there is a rare abnormality that Sean shares with the killer, meaning that they’re half brothers. However, Sean’s record indicates that he was an only child. Olivia and Lincoln go to talk to Sean’s mother, and Walter accuses Peter of tampering with Olivia’s memories. He warns that the impulse to make one happy is a dangerous temptation.
Olivia and Lincoln go to Florence, Massachusetts, to talk to Mrs. Keenan. She confirms that Sean was an only child, and explains that he was conceived by in vitro fertilization. The doctor who performed the procedure was Owen Frank, and he claimed that the donor was highly recommended and could have sired other children Mrs. Keenan explains that a reporter has called to talk to her about the process and Olivia realizes that it was Greene, the murdered man. Greene was killed before he could interview Mrs. Keenan, who still has the file on the IVF procedure she underwent. As she goes to get it, Lincoln and Olivia wonder if Greene was killed to stop his investigation.
At an assisted care facility, Dr. Frank sees the newscast about Greene’s death. Frank refuses to talk about it and asks to be taken back to his room.
Sean gets his appetite back as the meds wear off and Astrid watches as he eats in the hospital cafeteria. He says that she’s pretty and wonders if he can trust Walter. Astrid assures him that he can, and Sean tells her that he can hear voices but can’t understand what they’re saying.
Walter analyzes Olivia hair and puts honey into his tea. In her office, Olivia is trying to locate Frank but discovers that the records are incorrect. Peter comes in and she asks for his help, and then takes his hand and comments that he has a scar she doesn’t recognize. Peter explains that he got it in the last month and starts to take her hand, but then releases it. Walter comes in and sees what is going on, and tells them that he has a theory. He uses bees to demonstrate that certain animals use pheromones to communicate, and that other animals use other means. He believes that Sean and his half-brothers have a similar ability and are able to form a collective identity. Olivia gets a call confirming where Frank is and she leaves to talk to him. As Peter goes with her, Walter glares at him.
At the center, Peter and Olivia ask Frank about the clinic. He explains that he knows about Greene’s murder and that it’s not the first time that “he” has killed. The doctor explains that he hired someone three years ago to document his work, but that the man was murdered in a supposed mugging incident the day before he was to start. Frank believes that it wasn’t random and that someone wanted to keep him from publishing his work. He explains that he used recombinant DNA without telling his patients to try to make new and improved human beings. The process involved implanting animal-like instincts such as a hive identity and a heightened protective instinct. Now Franks believes that they are killing to prevent knowledge of their existence from becoming generally known. The doctor stored the clinic files at a storage facility and gives them the address, and informs them that he fertilized 200 babies with the recombinant DNA. Peter realizes that Frank used his own altered DNA and the doctor admits that it was the height of hubris for him to try and improve upon God’s work.
At the institute, Sean tells Astrid that he can hear the voice of one of the three killers and the man is in pain.
At a truck stop restroom, the killer rebandages his wound, wincing in pain.
As Lincoln returns, Walter finishes analyzing Olivia’s hair. The scientist immediately tells Lincoln to take him to the bridge so that he can meet with Nina Sharp. They go through to the Other Side and meet with Nina, and Walter tells her that someone is duplicating cortexiphan and giving Olivia multiple doses. He asks for the remaining samples, but Olivia says that they are locked up at Massive Dynamic and only she has access. Walter says that he is familiar with the remaining samples and will know if anyone tampered with them. When Nina calls to confirm, Lincoln tells her it’s better if they do it in secret and she agrees.
As Peter and Olivia go to Frank’s storage container in Back Bay, Olivia tries to explain that she feels confused because she feels close to Peter even though she knows her feelings aren’t real. She wants Peter to treat her like she knows him better than anyone else in the world. As they find the storage unit, Olivia remembers a similar container in Peter’s timeline that was rigged with plastic explosive. Peter remembers the incident but didn’t know that plastic explosive was involved, which means that Olivia isn’t receiving his memories. They examine the container door and discover that someone has broken in.
Sean hears the voices talking and tells Astrid that they’re preparing to kill Olivia.
One of the killers tries to run over Peter and Olivia with his SUV. He crashes and two others attack, but Peter manages to knock them out.
At the assisted care center, two of the killers enter Frank’s room and smother him with a pillow. The police arrive a few minutes later and find Frank dead.
Sean is trying to watch TV and turns up the volume up loud, and his mother turns it back down. Her son snaps at her and then tells Astrid that he can’t hear his “brothers” anymore. Sean assumes that they have shut him out of the collective, and that he is alone for the first time. Astrid assures him that what he has now is what is considered normal, and a crying Sean accepts what she says.
On their way back, Olivia pulls over at a gas station. She reminds him that in his timeline, they’d go home to one of their apartments after a case and make love, but she doesn’t know what to do now. Peter tells her that he’s been thinking about it as well, but that he betrayed his Olivia and doesn’t want to do so again. They kiss but then Olivia says that she needs to use the restroom and goes into the gas station.
At the vault, Nina opens the chamber and reveals that all 20 cortexiphan vials are present. However, Walter samples one and tells her that someone has replaced it with a substitute.
When Olivia doesn’t return, Peter goes into the gas station and discovers that Olivia has vanished.
Olivia wakes up and finds herself tied up in a room... with fellow prisoner Nina Sharp.