The cleaning lady at Liberty Island calls to tell Peter that Olivia disappeared before her eyes, and gave her a message for Peter that she's trapped on the other side. After Peter hangs up, Bolivia sleepily asks who it was, and Peter dismisses it as a telemarketer. She goes back to sleep, but Peter lies awake, watching the hours go by. Finally he gets up and goes through her belongings. He finally checks out her laptop computer after making sure that she's still asleep. When he locates an encrypted file, he starts trying to get in. Bolivia comes in and asks what he's doing, and Peter claims he's sending an e-mail to a friend in Corinth. He recites the line in Greek that Olivia passed on to him from William Bell, and Bolivia doesn't recognize it.
Once Bolivia goes back to bed, Peter fakes getting a glass of water and then goes back to the desk... and discovers that Bolivia has picked her gun up. She holds him at gunpoint, having realized she failed the test, and figures that the phone call tipped him off. Bolivia refuses to answer his questions and gives him a syringe to inject himself. As he prepares the syringe, Bolivia asks if he's going to come after him and kill her, and he promises that he'll get answers. If he finds out that she did anything to Olivia, he promises to kill her. Peter injects himself and is paralyzed.
Bolivia goes to the antique store and sends a message to her superiors, warning that her cover is blown and requesting extraction.
The next day, Broyles and Walter find Peter. Once he's back to normal, he explains what happened and insists they have to go to the Other Side to get Olivia. Walter warns that it's impossible, but says he might have a few ideas. When Broyles wonders what Peter was doing with Bolivia at that time in the morning, Walter tries to cover but Peter admits he was romantically involved with her. Peter then discovers that Bolivia took the wrong computer He shows them the encrypted file and figures it might be a clue to where she's going.
As Bolivia leaves the store, the owner figures that she's been told to wait. He admits that he's been waiting for seven years, but her people haven't kept their promise to restore his legs. Bolivia checks the laptop computer and realizes that she took Peter's.
On the Other Side, Colonel Broyles arrives at the Department of Defense building. Inside, Brandon meets with Secretary Bishop, and Bishop says that they can exchange Olivia for Bolivia to get their agent back. Brandon asks if they want him to send back Olivia live or dead, and says she has some valuable parts he can study without changing the mass. Broyles then meets with Bishop, and Bishop explains that they're ready to take steps to make sure that their world is the one that survives. He assures Broyles that Bolivia's mission was a success, and they share a toast to her safe return. As Broyles leaves, two orderlies take Olivia away. She begs him for help but he turns away.
On This Side at Harvard, Astrid and Peter discover that Bolivia had files on Olivia's debriefs, and she used them to pull off the impersonation. Walter comes in and apologizes to Peter for failing to find a way to get to the Other Side. Broyles arrives and informs them that they've recovered seventeen pieces of Bishop's device. That morning, Bolivia used her credentials to access the hangar where they were stored. She took one particular piece, and Peter figures that Walternate sent her to retrieve the piece he needed. If they lose Bolivia, then they lose their chance to get Olivia back. Walter is eating one of the baked goods that Bolivia brought him, and admits that he has no idea how to get to the Other Side. As he complains about Bolivia's feminine wiles, Astrid realizes that Bolivia went to the same bakery in the Bronx every time, and they figure that Bolivia knew someone there.
At the antique store, Bolivia gets a message from the Other Side. She then tells the owner that if he wants his legs, there's one more thing he has to do for her, and gives him a metal box.
Peter, Broyles, and Walter arrive and search the area around the pastry shop. Peter goes to the antique store and spots his computer on the counter. He forces the owner to show them the typewriter, and Walter realizes it's a device that contacts the other station. Peter checks the ribbon and finds a reference to Penn Station in Newark.
On the Other Side, Broyles is drinking at a bar and watching a retrospective on the first dimensional breach 20 years ago. As he goes, the bartender says that he's a hero. Broyles goes to Liberty Island and meets with Olivia in her cell. The colonel thanks her for not giving him up, and tells her that his son Christopher is doing better. Olivia figures that he's there to make himself more comfortable, and shows her the marks that Brandon and his scientists have drawn on her forehead. Before they make the swap, they'll cut out her brain and study it, and then put it back in. Olivia begs him for help, and Broyles insists that they're at war. In response, she says that everything happened that was because she came to rescue Peter, and that if she dies then This Side will strike back. Olivia insists that there must be a way to save both universes, and Broyles wonders if he can trust her. She says that if he can't trust her, there's no hope. An orderly comes in and prepares to give her a series of injections, and Broyles tells Olivia that there's nothing he can do and leaves.
Broyles and Diana go to Central Park and he explains that there have been thousands of deaths on their world, and he knows a way that may stop it. However, it could cost billions of others their lives. When he wonders who he is to play God, Diana says that she knew he was the right man to protect the world when they married, and she believes in him now.
On This Side, Peter, Walter, and Broyles drive to Penn Station. Broyles gets his men heading there, and asks Walter if he has any theories. Walter admits that he doesn't, and Peter isn't sure if they have any chance of getting her back. Broyles insists that she's strong enough to get back if anyone can.
On the Other Side, Brandon prepares to operate on the paralyzed Olivia. Broyles comes in and knocks him out, and then gives Olivia an adrenaline shot to help her shake off the paralytic. They go the lab and Olivia realizes that Bishop has synthesized Cortexiphan to send his soldiers to This Side and conduct their way. As the alarms go off, Olivia realizes that they've drained the sensory deprivation tank. She tells Broyles to go rather than betray himself, and she'll swim to Boston and get to the lab in Boston. Since Walter had a sensory deprivation tank, she figures that Bishop will as well. Broyles warns her that she won't make it since they've changed the harbor patrols, and takes her with him.
Secretary Bishop gets word that Olivia has escaped.
On This Side, Bolivia goes to Penn Station and has a final cup of coffee. A shapeshifter escorts her to the women's restroom and gives her a series of injections, while explaining that the transfer is scheduled for 23 minutes.
Peter, Broyles, and Walter arrive at the station, and split up to search for Olivia along with the Newark police.
A woman enters the restroom and is shocked to see Bolivia getting injections.
As Peter walks by the restroom, he sees Bolivia and the shapeshifter emerge. Bolivia fires into the air, panicking the commuters, and ducks back into the bathroom. Broyles arrives and orders in his team, and Bolivia emerges with the woman. She threatens to shoot her if they don't put down their guns, and Broyles and Peter comply. A girl runs up and calls out to her mother, the hostage. Peter what's going on and asks the woman to identify her daughter's name. When she doesn't answer, Peter shoots the shapeshifter in the head, killing it, and the police take Bolivia into custody. As they take her away, Peter asks her how they can get Olivia back. Bolivia says she doesn't know, but says that what was between them became something more than an assignment. He tells her that he doesn't believe her and lets the police take her away. However, he's surprised to see that her bag contains the photos of the two of them together.
On the Other Side, Broyles takes Olivia to Bishop's old lab. They prepare the sensory deprivation tank, but the soldiers track Broyles via his subcutaneous transponder. He gets Olivia into the tank and tells her that he has to hope, and that she has to make his sacrifice worth it. Broyles closes the tank and Olivia listens as the soldiers close in.
On This Side, Astrid is in the lab when Olivia emerges from the tank... and collapses.
At the station, Broyles has Bolivia put in the van for transport. Walter is examining some small metal pieces from the injection device, and thinks they look familiar. Broyles gets word that Olivia has returned, but was taken to the hospital after having a seizure. As the transition time arrives, the metal pieces vibrate and the ground shakes. Peter and Broyles run to the van and discover that Bolivia has disappeared. In her place is an equal mass of the alternate Broyles.
On the Other Side, Bolivia returns to Fringe Headquarters. Lincoln shows her his fully healed hands and face, and says it's like nothing ever happened. Agent Astrid asks if they've seen Broyles, who didn't go home the previous night.
On This Side, Broyles goes to the morgue and looks at his dead counterpart.
The storeowner meets with one of the Other Side's agents. He receives an injection that restores his legs, and gives the agent the box that Bolivia left him. In it is the missing weapon component.
Olivia wakes up and finds Peter at her bedside. He takes her hand and apologizes, and she says he has nothing to apologize for. Olivia tells him that if it wasn't for him, she wouldn't have made it back. Peter kisses her on the forehead.
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