Peter is still unconscious. Astrid tells Walter that the doctor hopes he won't have any permanent damage. Walter argues that the surge from the machine could've disrupted Peter's neural patterns, created memory deficits, aphasia, who knows?
On a freeway in Pittsfield, Massachusetts, lightning randomly strikes vehicles and the ground. It's happening all over, as far as the eye can see.
At the Massive Dynamic hangar, Sam Weiss tells Olivia that the machine's been tricked into thinking Peter's already inside. It's repelling anyone who tries to enter. It's frustrated, so to speak, which explains all this damage. It's not a doomsday device, but it's acting like one. He shows her the manuscript the First People books were based on. Unpublished pages depict a small rectangular box and a key. What's inside? A crowbar of sorts, which can pry open the forcefield long enough to get Peter in. Olivia asks if Peter will die then. Sam says the machine's supposedly indestructible, so Peter should be safe inside it.
Broyles tells Walter and Astrid about spontaneous dry lightning storms happening along the Eastern Seaboard. Walter wants to be with Peter, but Astrid protests. They need to solve this. Walter complains he even asked God for help, and got nothing! Astrid scolds that God helps those who help themselves. Walter says that was Ben Franklin's phrase and gets excited. Astrid's right. He needs his kite!
In the family crypt at Saint Arthelais Cemetery, Sam explains that he's not the first Sam Weiss as he and Olivia break into the tomb of his great-great-great-great-grandfather. His ancestor was digging for mastodon bones and discovered an ancient manuscript instead. The fifth Sam Weiss wrote the First People books. The third and fourth spent their lives searching for the manuscript's missing sections.
They find the box. Now they need the key. But Sam's doubtful. Through generations, no one ever mentioned the Other Side turning on the machine first. Olivia says that she's armed and wants the key. Now.
Peter wakes up, gets dressed, and leaves the hospital. He seems dazed. Hailing a cab, he gives the driver a New York City address: 42nd and Lex. The cabbie says that's a pretty steep fare from Pittsfield. Peter hands him his credit card.
Walter and Astrid discover that the Fringe events are clustered around two points: the MD hangar and Liberty Island, aka Department of Defense headquarters on the Other Side. Walter shows Broyles how the machines are creating a swathe of events between them - like two magnets creating a magnetic field, but across universes. He says if we move our machine to the same spot as theirs, we'll slow the destruction. It's crazy, but it's the only option.
Sam and Olivia retrieve the key. Inside the box is . . . a drawing of Olivia! Walter says it means she can turn off the machine with her mind. Telekinesis, says Sam. No way, says Olivia. But Walter reminds her about David Robert Jones. She defused a bomb by turning off some lights with her mind. Olivia's ability to cross over should work together with her telekinesis. She can control the machine Over There from Over Here. She practices on the typewriter Bolivia used to communicate with Walternate, but nothing happens. Walter says to focus on something specific: a word, a phrase.
A nurse finds Peter missing. He's left a note: "I am going home."
Walter tells a frustrated Olivia that he's learned to embrace the parts of his mind that are peculiar, broken. He understands now: That's what makes his mind special. And if Olivia would see how extraordinary she is, she could do anything. She tries again. Nothing. Astrid reports Peter's missing. He's used his credit card. But why's he in New York?
As the machine travels via barge to Liberty Island, Peter buys a silver half-dollar in a Third Avenue pawn shop. "It's my favorite," he says. "It always brings me luck." At Liberty Island landing, Peter tells a cop he needs to talk to his father: Walter Bishop, the Secretary of Defense.
The team goes to fetch Peter, but Sam can't come. Official personnel only. Later, the last Sam Weiss stands alone, gazing at Liberty Island and the lightning. A Newton's cradle clacks away behind him.
Peter knows that Walter isn't the Secretary of Defense. He's been confused, but it's temporary. Walter takes the half-dollar from Peter. Where did he get it? Never mind; time to turn off the machine. Olivia privately tells Peter she concentrated on a phrase, like Walter said, and still nothing. Then Astrid calls. The typewriter is repeating the same message: "Be a better man than your father."
Holding hands, Olivia and Peter approach the machine. She lets go, closes her eyes . . .
. . . and turns it off. The connections for Peter's limbs open.
On the Other Side, Brandon calls security. The machine is shutting down!
As Peter turns away, Olivia stops him. "I love you," she says. They kiss. He climbs into the machine, flashing back to many moments over many years. He puts his feet in. "Dear God," moans Walter. One arm goes in, and Peter looks at Olivia. More flashbacks. He puts his other arm in, closing the circuit. Power arcs through his body.
Peter opens his eyes. It's night. He sees fires, people running, and soldiers everywhere. A sign reads, "We Will Never Forget September 11, 2001/Dedicated to Their Memory September 11, 2021." WHAT? The Freedom Towers loom overhead. A soldier yells and tackles Peter as an explosion goes off. Peter spots a patch on the man's sleeve: Fringe Division. Where the hell is he? His shirt's bloody. The agent says sir, you've been hit. He shouts for a medic as Peter swoons.