At the hospital, Peter is still in a coma and Walter is sleeping at his bedside. Astrid comes in and tells Walter that the attending physician, Dr. Levin, plans to keep Peter sedated. However, Walter warns that they have no assurance what damage the Machine may have caused to Peter. Astrid suggests that they go for a walk and get some food, and Walter reluctantly agrees.
In Holyoke, Massachusetts, a boy and his family are driving along the highway when the boy, Nate, looks out the window and sees clouds gathering. The hairs on his arm rises and he starts to warn his parents. A lightning bolt strikes a car in front of them, and another one hits near their car as they brake to a stop. Nate's father Gary backs up the car and then gets out to investigate. He runs up to the overpass and sees dozens of smoking cars on the highway ahead as more lightning bolts strike down.
At the Machine hangar, Olivia explains to Weiss that their Machine was activated when the one on the Other Side was turned on. Weiss points out that only Peter can activate the machine and throws a pen at it. It's repelled and Weiss explains that the Machine already believes that Peter is inside, so it has established a force field to prevent anything else from entering. Weiss shows Olivia a "manual" to the Machine that he has, and explains that there is a key, and a device that can open the force field so they can get Peter inside.
Walter and Astrid return to Peter's room and overhear a doctor discussing the freak lightning storm and its victims, who are being brought in. Broyles arrives and tells them that similar storms have been reported up and down the coast. Walter refuses to go back to the lab and admits to Astrid that he's out of ideas. When he tells her that he asked God for help and got no response, Astrid points out that God helps those that helps themselves. Walter remembers that Ben Franklin originated the quote and goes off to get a kite.
At Saint Arthelais Cemetery, Weiss explains that he's not the first Sam Weiss, and the fifth Sam Weiss found the manuscript and wrote the First people books. They open that Weiss' crypt and remove the locked box containing the lever, but Weiss has second thoughts. He warns that it's only to be used if the machine is malfunctioning, and tells Olivia that no one anticipated the Other Side turning on the machine. Olivia insists that Weiss take her to the key.
At Harvard, Walter sends a kite up with wiring to monitor the electrical readings. Astrid monitors the equipment while Walter takes two lightning strikes. He realizes that there is a missing variable and they have to account for repetition, and tells Astrid to pack up everything and go to the lab.
At the hospital, Peter wakes up, gets dressed, and goes out into the hallway. He wanders down the hallway and sees all of the burn victims in the ER. A nurse asks if he's all right, and Peter can't remember who he is. She's called away by an emergency and Peter continues walking outside, where a vast storm has gathered in the sky as lightning bolts strike everywhere.
Peter picks up a cab in Pittsfield, Massachusetts, and tells the driver to take him to an address in new York. When the driver points out that it's a steep fare, Peter gives him his credit card and they depart.
In Boston, Weiss drives to the Whitley Museum, which is in the middle of a lightning storm. He warns that the key is inside, and they talk to the museum director, Christine Albright. He points out the key in the Native American wing and asks for the quickest route. Albright asks Olivia to be careful and they prepare to go inside.
Walter starts checking all the spots where lightning has struck twice so they can measure the frequency. When they compare it to the other vortex indicators, he believes they'll have an answer. The pattern indicates two foci and a rift between them. One foci is where their Machine is, and the other is Liberty Island, and Walter realizes that it is where his counterpart is located.
Walter goes to Broyles' office and offers a demonstration of magnetic patterns. His demonstration shows that the second Machine must be at the DoD headquarters on the Other Side. Walter suggests that they move their Machine to the same spot as the other one to stall the destruction. Broyles points out the risks and notes that the two overlapping machines will cause more damage in the vicinity. Walter admits that it sounds crazy, but it's their only option.
Olivia and Weiss get to the Native American wing and find the case containing the key. Lighting smashes through the skylight and they take cover. Olivia goes to disable the alarm while Weiss removes the stone tablet from the case. They head for the exit but a gate starts coming down. The controls are short-circuited by the lightning, so Weiss throws a piece of rock, knocking an urn under the gate to block it so they can escape. Outside, Weiss removes the key from the artifact and gives it to Olivia, but warns that he doesn't know how it works. Olivia examines the primary mechanism, which opens at her touch. Inside is a scroll with a picture of Olivia on it.
Weiss and Olivia go to Harvard and show Walter the drawing. He speculates that Olivia also has a connection to the Machine, and she must be able to turn off the force field. Walter rolls it and realizes that the lines indicate Olivia can use telekinesis to shut down the force field. However, he warns that she'll have to interact with the machine on the Other Side. However, she should be able to use her two abilities, to transition and to move things with her mind, to move the Machine on the other side. Olivia points out that she doesn't have any training, and Walter admits that she'll have to start small. He sits her down at the typewriter and tells her to visualize the typewriter on the Other Side and type out a message. Nothing happens at first and Walter tells her to concentrate and be patient.
A nurse goes to Peter's room and finds him gone. He's left a message: "I'm going home."
Olivia has had no success and suggests that Walter give her cortexiphan. He warns that it would only harm her, and she has to draw upon the abilities inside of her. When Olivia says that she can't, Walter tells her that he's come to embrace the broken parts of his mind which make him special, and he can understand what she's going through. Olivia is skeptical but tries again without success. Astrid arrives and tells them that Peter has disappeared from the hospital.
As the government brings the Machine to Liberty Island, Peter tries to find a pawnshop that he vaguely remembers. A pedestrian directs him to the shop and Peter asks to see the rare coins on display. Peter goes through them and picks out one particular coin, a silver half dollar that he says is his favorite because it always brings him luck.
At the lab, Astrid calls and confirms that Peter isn't at the Bishop house. Walter snaps at her and then apologizes, admitting that he's scared. Olivia confirms that Peter has used his credit card to pay for a cab and a coin in New York.
Peter goes to Liberty Island as the authorities evacuate the area. He tells a guard that he needs to talk to Walter Bishop… the secretary of Defense.
Olivia talks to Weiss, who says that he intervened when he shouldn't have. Broyles arrives and tells them that they've found Peter at Liberty Island, and the Machine has been delivered there. They prepare to leave but Broyles says that Weiss will have to stay behind. He wishes Olivia luck as she goes.
Later, Weiss goes to the shore across from Liberty Island and watches, as his executive ball toy continues to bounce balls back and forth. Meanwhile, Walter and Olivia greet Peter, who remembers that there are two of each of them. Walter examines him and confirms that he's fine, and his real memories of This Side are coming back. The last thing he remembers is entering the Machine. Walter sees the half dollar and starts to ask Peter where he got it, but the island shakes. They go to the Machine and Walter warns Broyles that as long as it's on, there's nothing they can do. Meanwhile, Peter and Olivia go over the new drawing and she explains Walter's plan and her inability to contact the Other Side. When she says that she was concentrating on a particular phrase, Peter asks what it was.
At the lab, Astrid hears the typewriter start typing. She examines it and then calls Olivia to tell her that it's typing the message, "Be a better man than your father.
As Broyles orders evacuation of all non-essential personnel and the quakes grow stronger, Olivia prepares to contact the Machine on the Other Side. She worries that she can't do it, but Walter assures her that he and the person who made the drawing both know that she can't fail. Meanwhile, Peter looks up at the Machine and takes Olivia's hand. They both admit that they're not ready, smile, and then approach the Machine. Olivia concentrates and after a few minutes, the Machine shuts down and the devices to hold Peter open.
The Other Side
Brandon realizes that something is happening to their Machine and notifies Secretary Bishop.
As Peter goes to enter the Machine, Olivia tells him that he loves her and they kiss. He tells her to wish him luck and then enters the Machine. It fastens him in and energy surges through him…
Peter wakes up on a street as people run in terror. Buildings are burning and soldiers are trying to contain the rioters. Peter finds a memorial to the fall of the Twin Towers... on September 1, 2001, and dedicated in September 2021. A soldier with a Fringe Division patch runs over and addresses him as Agent Bishop, and Peter realizes that he's been wounded.