As Peter travels over the city by helicopter he sees that this alt-Manhattan is very different from the one he knows. Areas where Fringe events took place are quarantined, where people are trapped inside a weird, amber-like substance but are ruled legally dead. He arrives at the Department of Defense, housed on the same island where the copper-coated Statue of Liberty stands. Meanwhile, an assistant tells Secretary of Defense Walternate that a high priority individual was admitted to New York General Hospital -- and it is the Secretary himself. Walternate does not seem shocked. Colonel Broyles calls Bolivia with the assignment.
After searching other hospitals, William Bell and Olivia get to New York General looking for Walter. Olivia gets to Walter as Bell stalls the just-arrived Bolivia and Charlie. Walter shows off the accelerated healing techniques in this world. He's rejuvenated and his gunshot is nearly healed. Bell drives up to help them escape. He and Walter exchange the gruff greetings of old rivals. Bolivia finds that Walter is gone and is shocked when she sees a blond version of herself helping someone who looks like Walternate.
Walternate explains to Peter that his world experienced much worse side effects than the soft spots in the other. They are now reduced to quarantine zones. Walternate blames all of this on Walter. He also says that the machine from the schematics is something he thinks can heal both worlds, only its power source is still not working. Peter is thrown for a loop when Bolivia comes in, and he tells her she reminds him of someone he knows with different hair. Walternate confirms for Bolivia that the invaders are the parallel versions of themselves, but they are "monsters in our skin" who cannot be trusted. He explains that Peter was kidnapped by "them" but is now returned.
Bell, Walter and Olivia hide out and discuss the issue of crossing back without the power of the other Cortexiphans. If Olivia can provide a crack to that door, then Bell is sure that Walter can create a "doorstop" to keep it open. Olivia interrupts Walter and Bell's bickering to say she's going to find Peter. Since all phone communication is monitored, they agree to meet back at the opera house in twelve hours. After Olivia leaves, Bell wistfully notes to Walter that "she may be our greatest achievement."
Bolivia brings Peter to a high-tech apartment that Walternate set up for him. It's decorated with Bishop family photos. Bolivia tells him that his kidnapping as a child was a well-known story, and he will be famous now that he's back. Bolivia asks Peter what "she" is like, and he describes Olivia as haunted. Realizing the distance between them, Peter says that the two women are nothing alike.
Bell drives Walter through the New England countryside. It's a barren wasteland. Walter is responsible for what it has become. They get to Harvard University, where people are frozen in time in an amber-filled quarantine surrounding part of the campus. Bell takes him to Walternate's lab, which is where Walternate unsuccessfully tried to create a way to cross over. Bell explains that on This Side, his alternate version was killed in a car accident at a young age, so the Other Bell and Walternate never met. Bell says that he only came to This Side to prevent the war and he created the shape shifters in order to stay close to Walternate. Yet Walter retorts that Bell is only benefiting himself by fueling the war and founding Massive Dynamic.
Bolivia returns to her apartment to find Olivia there, demanding to be taken to Peter. Yet Olivia softens when she sees a photo of her mother, who is still alive. Bolivia says that her sister died in childbirth. Olivia asks Bolivia to trust her. "I'm you," Olivia pleads. Bolivia pulls her own gun and orders Olivia to drop her weapon. Olivia lunges at her, knocking the gun down. The two women fight, evenly matched. Yet Olivia is able to knock Bolivia out.
Walter and Bell find a device that could be the "doorstep" in the lab. As they steal it, Walter asks why Bell removed pieces from his brain, taking away memories. "Let the past be the past," Bell replies.
Olivia dies her hair to look like Bolivia and dresses in her clothes. She ties up Bolivia and uses her tiny personal handset to look up Peter's address. Olivia exits the apartment to find Charlie there. Thinking she's Bolivia, he says they are assigned to check out Walternate's old lab. Olivia says they have to move Peter, and Charlie is shocked that Peter has even been found.
Peter examines the power source at his apartment. He speaks into a recording device as he notes that the device reflects a human genome -- his own. The device clamps onto his hand and seems to power on. He's interrupted by Charlie and who he thinks is Bolivia. She hands him the Observer sketch and warns him of the danger that would occur if he returned "There." Charlie is confused, and Olivia knocks him out. Peter realizes that this is Olivia.
Peter explains that Walternate told him he was the key to fixing all of This Side's problems, but he now knows that he was brought back to destroy the other world. Peter is confused because he doesn't know which Side he belongs on. Olivia says he must come back because he belongs to her. They kiss.
Bolivia escapes from her binds and meets Walternate at the Fringe headquarters. They find that Olivia is headed to the opera house, and Colonel Broyles sends his teams out to get her.
Walter and bell lug the device into the opera house as Olivia and Peter pull up. Bell breaks the tension between Walter and Peter by introducing himself and cryptically saying, "You're holding up better than I would have expected." The police arrive, and Bell fends them off with an advanced weapon of his creation and phosphorous grenades that the Fringe team doesn't have. It buys them time as Walter and Peter set up the device inside the theater.
Bolivia and Colonel Broyles get word from Walternate and nod to each other secretly. Broyles has his team stand down and Bolivia shoots at Bell, who falls down and passes out. Bell wakes up to find Olivia over him. The street is devastated and empty. Olivia says she used one of the grenades, and she leads Bell into the theater.
Walter gets the device to turn on, but Olivia doesn't have enough power to keep the "doorstop" open. Bell says that he will be the power source. He explains that he has crossed over so many times that his atoms are ready to split apart at the slightest provocation. Walter realizes the gravity of Bell's offer, and says, "Thank you, old friend." Bell finally confesses that he removed parts of Walter's brain because Walter asked him to. Walter was afraid of what he was becoming.
Suddenly, the Fringe team starts to raid the theater. Bell uses his own energy to power the doorstop, and in doing so, his body explodes. Walter, Olivia and Peter find themselves standing in the calm of the opera house -- back on their Side. The invading Fringe agents have disappeared. The real Broyles welcomes them home.
In the lab, Walter asks Peter if he's back for good. Although he cannot see it Walter's way, Peter says he appreciates that Walter has crossed universes twice for him. Walter is overcome with emotion in Peter's forgiveness.
Olivia shows up at the antique office equipment store. She's looking for a Selectric Model 251. She is given the key to the back room. It's really Bolivia who crossed over! She puts in a piece of paper and types "Infiltration Achieved. Awaiting Orders."
On The Other Side, Walternate goes to a cell where Olivia (still with Bolivia's hair) is locked inside. She cries to be let out, but Walternate just shuts the door to keep her locked in.