Peter successfully enters the machine with Olivia's help, and is transported to the future days where Walternate's universe is the one which has been destroyed. Walter learns about the origins of the machine and its ultimate purpose and sends back Peter to change his choice but gets lost in time warp.
In 2026, only our universe has survived after the destruction of the parallel universe but with damages since they were inextricably linked together. The Fringe Division uses amber to contain the vortices and are investigating the terrorist group called "End of Dayers" led by Moreau that are creating more vortices. When a cylinder is retrieved by the Fringe Division, Peter asks Broyles to release Walter to help to understand how it works. Soon he finds that it is an advanced technology and Peter meets Walternate that promises him that he will suffer a pain for what he has done destroying his universe. Soon he kills Peter's beloved wife Olivia and Walter tells that there is a chance to change Peter's decision in 2011. Will his plan work?
- Future Agent Bishop is wheeled into the ER by Astrid and Fringe Division. He's bleeding by they tend to him.
Fringe Medical, New York, May 20, 2026
A girl comes to visit Peter in the hospital -- she's young Agent Dunham, Olivia's niece Ella. Olivia explains they think it's the End of Days. Peter hugs Olivia hello. He wants to track Moreau.
Ella asks him if he remembers what he was saying when he was in the field, about the machine and being from the past. They look at the TV, there's a stage three tear at One World Trade Center.
The terrorist Moreau is claiming responsibility. We see his picture, then we see him with two men inside the Brooklyn Philharmonic. He listens at the door then places a canister and his henchman shoots the guard. They set up other canisters. They detonate, leaving nothing but ashes.
Future Peter, Olivia and Ella check it out. There are bodies sheared in half and rubble. Astrid reports the alarm was disabled. One canister remains -- a dud. Peter is excited to examine it.
Fringe HQ, Boston
Peter examines the canister with Astrid, he tells Olivia it doesn't seem like it should be working. He says there's only one person who can understand it. Walter. He says it's past time to call in markers to see him.
Peter visits Walter in jail. Walter is brought out, he's aged and bedraggled, like when we first met him in the mental hospital.
"It must be bad if they're letting you see me," Walter says. Peter says it is. A wormhole opened in Central Park, but they ambered it over. There are tons of gamma rays. The wormhole was to 250,000,000 years ago.
Peter shows Walter why he's come. He explains the canister is a light bomb used by the End of Dayers to try to rip holes in the fabric of the universe at the soft spots, to accelerate the End of Days. Peter wants to trace the parts.
Walter says he'd need his tools to help, but they both know that won't happen.
Peter waits to see Senator Broyles, who now has one milky eye. There's a report on TV about a vortex opening in the Thames.
Peter shows Broyles the light bomb and asks for a temporary furlough for Walter. Broyles says there's no way, because Walter is responsible for everything, even if it wasn't his intention.
"If what we lost in Detroit still means anything to you, just give me one chance. It's all I'm asking," Peter says.
Peter brings Walter back to his lab at Harvard, which has been cleared out and taken to evidence. Olivia's getting it back.
Walter is shaved and cleaned up, and we can see half of his body is now partialy paralyzed. Olivia comes to see him. He congratulates her very belatedly on her wedding.
A mover starts to drop one of Walter's boxes and as he's yelling at him, it suddenly stops in mid-air and floats gently and safely to the ground.
Olivia explains that she learned to control her powers a few years ago.
Moreau meets with a man on a park bench late at night. Moreau mentions the man's world was destroyed by a wormhole.
Moreau explains the light bomb has twice the yield of the device they used last night, and he followed his specifications. It's Walternate, and he says soon our world will join his.
Harvard Peter visits Walter and brings him red vines. Walter can't make any sense of the technology. He says they can't stop their destiny, which they triggered when they used the machine. He didn't understand the worlds were inextricably linked and without one the other can't exist.
"When their world was destroyed, that was the day we sealed our fate. For all intents and purposes, that was the day we died," Walter says.
Walter asks if Peter has seen Walternate. Peter says he's become a recluse. Walternate came over to save his world and got stuck when his was destroyed.
Walter blames his hubris for what happened, but Peter reminds him he was the one who got in the machine. Walter thanks him for speaking at his trial, but calls himself " the most reviled man in the universe."
At home at night, Peter makes Olivia dinner. There's kid's art on the fridge -- from a neighbor girl. They talk about kids. He asks if she wants to reconsider. He thinks they can still have a bunch of kids, even with how the world is.
The next morning, Walter calls Peter excitedly -- he's figured out they're splitting atoms. He knows a way to track it using the radioactive signature.
Peter and Olivia head out to campground where the signature was detected. An agent brings Peter a small piece of metal but instead of showing it to Olivia he looks at it alone -- it's a key box with a key inside.
Moreau and his goons bring canisters to the amber in Central Park.
At Fringe Division an alarm goes off for Central Park.
At the lab, Walter explains the light bomb technology to Olivia and her niece. She gets the call about the security breach at the worm hole.
Reiden Lake Peter arrives at his family's old summer house. His phone rings but the call drops. He uses the key and goes inside, gun drawn.
He finds Walternate calmly waiting for him. Peter puts down his gun and sits. Walternate says he couldn't just call. Peter thinks letting him know Moreau works for him was a way to get his attention. Peter figures out Walternate designed the light bomb.
Walternate is bitter and angry, saying he came on a mission of mercy. He blames Peter for using the machine, but Peter reminds Walternate that he started the machine on his side first.
"You destroyed my universe son, now I'm going to destroy yours -- but not all at once," Walternate tells him.
At the wormhole, Olivia reports to the scene. She's giving orders when there's a giant flash of light. She comes to in time to see a vortex forming in front of her.
Back at the lake house, Peter apologizes to Walterate "for destroying your people -- our people." He says if he could take back that choice, he would, but it's no excuse for what Walternate is doing.
Peter takes out handcuffs and says Walternate has to come with him.
Walternate says if he was really there he might kill Peter, so it's good he's not. Peter realizes he's talking to a hologram. Walterate says he going to start by killing someone Peter loves, then he ends the transmission.
Cut back to Olivia giving orders at the wormhole, reaching into her car for her phone and turning around to see Walternate standing in front of her. He raises his gun and shoots her dead between the eyes.
Later, Peter speaks at a night time beach funeral service for Olivia. Nina Sharp, Broyles and her niece are there, as is Walter, in prison garb.
They send her casket out to sea on a pyre.
In the car after, young Agent Dunham tells Walter they're still trying to seal up the wormhole. Walter gets an idea and asks to be taken t his lab.
Peter drinks alone in his house. He cries over the drawing of he and Olivia.
The next morning, Walter is done with his diagnostic. He tells Ella he can't understand her loss and would change things if he could.
On his computer, Walter sees a simulation of a wormhole and thinks he has the answer.
He arrives on Peter's doorstep with calculations. "Peter I was wrong, it's not too late -- we can save both worlds," he explains. Walter says they can make a different choice. He shows Peter the old machine drawings.
Walter says it always bothered him not being able to figure out how the parts ended up millions of years ago. He realizes he sent the machine back through the wormhole.
He can't undo that because it's already been done, but now he can find a way to bring Peter's consciousness forward so he can witness what happens if he gets in the machine.
Back with Peter in the machine. He's been in it for 60 second and Broyles, Olivia and Walter wonder what to do.
On the other side, Brandon show Walternate the machine turned itself on and the soft spots are getting worse. He asks for Olivia. He thinks she can turn it off.
She realizes the other side put Peter in their machine and now they're the ones who are going to get destroyed.
On our side, they race to get Peter out. Suddenly it slows down and Peter snaps out of it. He looks at Olivia and says "Olivia, you're alive."
Then he closes his eyes and does something and the two sides are face to face in the same room, Fauxlivia to real, Walternate to Walter. Peter gets out of the machine and tells Olivia he understands now.
Peter tells Walter they're the First People's and they sent the machine back.
He tells Walter and Walternate that the worlds are linked and you can't destroy one without harming the other. So he tore holes in both universes and they lead to this room, a bridge so they can work together.
Suddenly, as he's talking, he disappears, leaving Walternate to scowl at Walter that it's his fault. Olivia suggests the damage is done, "so maybe it's time we start to fix it."
Outside the Statue of Liberty, a group of Observers stands staring. One Observer tells the other: "You were right, they don't remember Peter." The other replies: "How could he? He never existed, he served his purpose."