In the year 2026, the injured Peter is taken to a hospital by Fringe Division and Astrid assures him that he'll be fine.
Outside, Ella Dunham tries to get through to see Peter, but admits that she was just promoted. The receptionist assures her that Peter will recover. Olivia comes up to meet with her niece, and says that they think that Moreau, an End of Days terrorist, is responsible. Peter comes out and assures them that they'll fine, and Ella asks if he remembers what he was saying in the field about being from the past. He confirms that he remembers Olivia informs them that there's a stage-three tear at the World Trade Center and they've initiated amber protocol.
Moreau goes to an opera house with two of his men. He listens to the music briefly and then has his men set up cylinders in the lobby. When a usher comes over, they shoot him dead and leave. Once they're gone, the devices activate and the opera house disappears.
The Fringe team arrives at the crater where the opera house was located, and where the medics are bringing out the remains of the audience. They find cylinder that didn't activate it, and take it back to Fringe HQ in Boston to examine. Peter is examining the device when Olivia comes over. He informs her that according to all the readings, the device shouldn't work at all. They realize that Walter is the only one who can help them, and Peter asks if Olivia has any markers they can call in.
Later, Peter goes to a prison and meets with Walter… a prisoner. Walter realizes that they must be in trouble if Peter has come to see him, and they talk about how a massive wormhole opened up in Central Park. Peter confirms that the wormhole radiation indicates a passage in Central Park that extends 250 million years into the past, and Walter asks about Olivia. Walter's son then shows him the cylinder and explains that the terrorist group End of Days is using it on weak spots in the fabric of reality, and asks Walter for his input. Walter says that he needs his tools, and they both know that isn't going to happen.
In Washington, Peter meets with Senator Phillip Broyles and shows him the cylinder. He asks Broyles to grant Walter a temporary furlough, but the senator notes that the entire globe is disintegrating and Walter is responsible. Broyles admits that he knows that Walter didn't intend to cause global devastation, but everyone has lost someone due to the breaches. Peter insists that they can prevent future casualties if they can understand the technology, and reminds Broyles of what they lost in Detroit.
Broyles grants the furlough and Peter takes Walter to the lab in handcuffs. Walter is happy to hear that Astrid is now a field agent since she doesn't have to care for him, and asks Peter for permission to look in his old office. As he settles in, Olivia arrives to see him and they embrace. Walter offers his congratulations on her marriage to Peter and admits he always wanted a daughter. A worker knocks a box onto the floor and Olivia telekinetically catches it, and admits to Walter that she learned how to control her abilities several years ago.
Moreau meets Secretary Bishop by the river and gives him a new and improved version of the device built to his specifications. Bishop tells Moreau that his next target is the wormhole in Central Park and says that soon this world will join his.
Back at Harvard, Walter warns that their worlds are linked and when the Other Side was destroyed when they activated the Machine, it spelled the end of their world as well. Walter asks Peter if he's seen Bishop, and Peter admits that Bishop became a recluse after he was trapped on This Side when the Other Side was destroyed. Peter notes that he's the one who destroyed the Machine, but Walter points out that the court found he was innocent because he believed he was saving their world. Walter thanks him for his efforts and Peter says that no matter who was at fault, Walter is still his dad.
At home, Olivia and Peter enjoy supper, and Olivia asks how he's doing. Peter says that he's fine, and looks at the drawing a neighbor child made of them having a child. He asks Olivia if she wants to reconsider, and figures that they'll have several children despite what the world is becoming.
The next morning, Walter calls Peter and says that Moreau is splitting atoms using Strontium 90, a radioactive isotopes. The radiation will leave a trace and they can follow it to the source. Peter has Science Division check the radiation sensors, and the trail takes them to a campground. There's no sign of a lab, and Olivia goes back to check the reading. An agent finds a small black key case and gives it to Peter, and he quickly hides it before Olivia can see it.
In Central Park, Moreau goes to an amber containment zone and prepares two of the cylinders.
At Fringe Division, Astrid arrives at her desk as they receive a breach alert.
Walter tells Olivia and Ella that the technology is 15 years ahead of their time, and he has no idea where the parts were made. Olivia receives word of the breach and a possible Moreau spotting.
Peter goes to Reiden Lake and the old Bishop cabin. He receives a call but the caller hangs up and there's no indication of the signal. Peter then uses the key from the case to open the cabin door and go inside. He finds Secretary Bishop waiting for him. Bishop says that he lost everything, and he came to This Side to ask for help. He blames Peter for destroying the Other Side, but Peter points out that Bishop activated his Machine to destroy This Side. Unimpressed, Bishop says that soon everyone on This Side will experience the same loss that his people did, and Peter will lose everything as well… but not all at once.
Olivia and Ella arrive at Central Park. As they mobilize, there's a flash of light and everyone falls to the ground, unconscious. Olivia wakes up first and sees a wormhole in the middle of the park.
Peter apologizes for the suffering that he has caused Bishop, and for destroying their people. However, he says that what happened is no excuse for Bishop wiping another world. Peter takes out a pair of handcuffs and asks him to come quietly, but Bishop says that he's a hologram and that he's going to start teaching Peter about loss by killing someone he loves. Peter confirms that Bishop is a hologram and leaves.
At Central Park, Bishop shuts down the hologram projector, gets out of his car, and shoots Olivia in the head, killing her.
Later, Peter speaks at Olivia's funeral, where all of her friends have gathered. Even Walter is there, heavily secured. They send her out to sea on a funeral pyre.
Later, Ella is driving Walter back through New York City, and traffic is blocked by emergency operations to seal the Central Park wormhole. He gets an idea and asks Ella to take him back to his lab.
In his apartment, Peter is drinking heavily. He looks at the neighbor child's drawing and breaks into tears.
Walter runs a series of diagnostics and reminds Ella that she used to call him "Uncle Walter." She says that she doesn't remember much from before it got bad, and he offers his condolences. Walter says that he'd do anything to go back and change things, but Ella says that he can't and that there are no happy endings. She then says that she remembers Gene the cow, and how she had kind eyes. The diagnostics finish running and Walter finds what he's looking for.
Peter is at home when the MPs bring Walter to him. He explains that Peter needs to go back and change history, with Olivia as their failsafe. Walter has spent the last 15 years trying to figure out where the pieces came from, and has finally realized that he sent them millions of years into the past through the Central Park wormhole. Peter suggests that they never send the pieces back, but Walter warns that he can't alter history. He can't make a difference choice, but Peter can make a different choice if Walter can bring his consciousness from 2011 into the present of 2026 to see what will happen if he makes the wrong choice. Walter warns that they have no idea what the cost might be, but it can't be worse than losing Olivia. Peter agrees and asks what he needs to do.
In 2011, Peter has been in the Machine for 60 seconds, and his heart rate is accelerating. Walter has no idea how to safely remove him.
The Other Side
Ryan warns Secretary Bishop that the soft spots in their world are getting worse. He has Bolivia brought to him, shows her the drawing, and asks her to stop the Machine. She realizes that the people on This Side outsmarted him and that their people will be destroyed. Peter starts to appear in the Machine.
Olivia climbs up to Peter's position and he starts to revive. Everything fluctuates and then the two sides merge as Peter smiles. The Machine releases him, and the individuals from both sides contemplate each other. Peter says that he understands, and tells everyone that the Machine came from the future. He has seen the future, and that if one side dies then they all die. Peter tells them that he's torn holes in both universes, and they lead to the hanger so that they can work together. Peter starts to explain, but then fades and vanishes. Bishop tells Walter that he's caused the deaths of thousands, but Walter insists that it was an accident. Olivia says that whatever has happened, they need to work together to fix things.
Outside the Statue of Liberty, which has merged into a version containing components of both worlds, the Observers have gathered. They confirm that no one remembers Peter because he served his purpose, and now he doesn't exist.