At Olivia's apartment, Peter and Lincoln find a spy camera in the overhead light, with a memory disk that stores images on a 60-minute loop. Peter thinks he can find something on it.
David Robert Jones has imprisoned Nina and Olivia at an abandoned hospital. Nina tells Olivia that, just before being abducted weeks ago, she saw a woman who looked exactly like her. Jones enters with a minion, whom we eventually learn is Leland Spivey. He says he's waited so long to meet Olivia, and she informs him that they've already met. She watched him die, and she's looking forward to seeing that again. Puzzled, Jones replies that Olivia is not the first to say that.
Jones has indeed been giving her Cortexiphan, which has been causing her migraines. He knows her abilities are triggered by intense emotions. Leland jams a handheld drill into Nina's mechanical arm as she howls in pain.
In Boston, December meets with three other Observers. Only September can explain what happened with Peter Bishop. When he surfaces again, he will face the consequences of his disobedience.
In an FBI interrogation room, Nina, Broyles, and Lincoln spar over Olivia's disappearance. Nina insists that, before yesterday afternoon, she hadn't visited the Massive Dynamic deep containment facility in years. But the logs and MD security say she accessed it twice within the past three months. Nina says it must've been a shapeshifter. But then she'd be dead, says Broyles. Nina wants her attorney.
At Harvard, Peter scans the disk for useful images. Walter is upset. He warned Peter not to succumb to temptation. Whatever consciousness Olivia appears to be manifesting, she's not who Peter thinks she is.
Jones raises a shutter covering a window into another room, where Nina's strapped into a rack wired to a car battery. He shows Olivia a familiar wooden box (from the Season 1 episode "Ability"). She thinks that he wants her to turn off the lights with her mind, like before. This time, he wants her to turn the lights on. The torture of Nina is awful, but Olivia can't do it. Jones gives her an hour to rest.
Peter spots a face on the disk: Leland Spivey, who died three years ago. He must be from the Other Side. Peter guesses Jones is trying to activate Olivia again. Walter wonders why. Peter says they never knew, but maybe it's for the same reasons now.
Suddenly, September appears and says yes, his goal is the same. He collapses, bleeding from a bullet wound in his chest. Peter asks about Olivia, and September says, "She needs you."
Olivia tells Nina that Jones' plan isn't working, because the Cortexiphan has blurred her memories of Nina. To sharpen them, they discuss how Olivia first called her "Nina," instead of "Miss Sharp," on their first night together. But it's not enough: The only person this ever worked with is Peter. Surprised, Nina says, Peter Bishop? Suddenly, she convulses in agony. Jones' minions take her out.
Once outside, Nina is fine. She coldly tells Jones that Olivia can't be activated unless Peter Bishop is present.
As Walter and Astrid tend to September, Broyles reveals what the Observer told Olivia weeks ago - that she would die in every possible future. But now the Observer is dying. Peter goes into September's mind.
September has much to tell Peter, including his name, a code designation of his scientific team. The Observers are, or were, human - many generations from now. The war between universes drastically altered destinies and brought about a child who was not meant to be: Peter's son, Henry, born to the wrong Olivia Dunham. Like Peter, the child ceased to exist when Peter used the Machine.
September suspects Peter returned because of the Olivia Dunham from whom his shared future was meant to spring. If Peter finds her, everything will be as intended. Then he says, "They are coming." He wants Peter to do something for him, but Peter insists on knowing how to find Olivia. For that, says September, you need only to go home.
Peter comes to in the lab, and September vanishes. Peter wonders if he literally just needs to go to his house. He does - and is captured by Leland.
As the shutter rises, Olivia sees Peter strapped into a chair, with Nina behind him in the rack. Jones pretends he eavesdropped and heard what Olivia said about Peter. Leland threatens Peter, and Olivia turns on one light, then all of them. Soon electrical bolts are zapping all around. Also, Olivia knows this isn't her Nina: The first time she called Miss Sharp "Nina" was actually right after her high school graduation. Jones and Nina flee, and Leland fries.
Olivia tells Peter she thought she could do what she did as a child if they brought him to her. She has a brief seizure. They find Jones, just as Nina disappears through a portal. Olivia shoots him through the throat, but he smugly says there are some fringe benefits to having one's body reassembled on an atomic level. He escapes through the portal.
Peter helps Olivia outside and phones Lincoln for help. Now convinced that he really is having an effect on her, he says it was a mistake to believe she was his Olivia - a mistake he'd promised to never make again. This time, when he looked into her eyes, he saw what he wanted to see. But his Olivia's still out there, waiting for him. Sorry, but for now it's better if he stays away.
It starts raining. Heartbroken, Olivia asks where he's going. "Home," Peter says. "I have to go home." He walks away.