Walter is standing vigil over Peter when Astrid arrives. She passes on the doctor's report that Peter should recover, but Walter warns that the surge from the Machine could have caused any number of different trauma. Astrid convinces him to take a break for food.
A teenager, Nate, is listening to his MP3 player as his parents drive their car down the highway. The boy notices strange clouds forming on the horizon and the hair on his arms rising. He starts to tell his parents what he's noticed, but is interrupted when lightning hits the car ahead of them. Gary pulls over and another bolt strikes directly in front of the car. He backs up and then goes to the nearby overpass and looks out as lightning slams down repeatedly, hitting the cars ahead.
At the hangar, Sam says that the Machine wasn't supposed to start on its own, and only Peter can operate the Machines on either side. Sam throws a pen at the Machine and a force field repels it, and he explains to Olivia that it's been tricked into thinking that Peter is already inside. He then shows Olivia the manuscript that the First People books were published on, showing her a picture of a bar-key that opens a box, and inside is supposedly a lever that can shut down the Machine. Once Peter is inside, he'll be safe and can shut down the Machine.
As Walter and Astrid return to Peter's room, they see the victims of the lightning storm brought into the ER. Walter realizes that it's getting worse, and Broyles arrives to tell them that 25 people have been injured in dry lightning storms up and down the East Coast. Ignoring Astrid's objections, Walter prepares to go back to Peter's room rather than investigate the phenomena. When she quotes from Benjamin Franklin, Walter gets an idea and decides to investigate and understand the phenomena by getting a kite.
Sam takes Olivia to Saint Arthelais Cemetery where his great-great-great-great grandfather, the fifth Sam Weiss, is interred. They open it and remove the box, but Sam worries that he may be acting prematurely. Nothing he's read has indicated that the Other Side would activate their Machine.
At Harvard, Walter flies a kite in the storm while Astrid measures the readings. The kite is struck twice by lightning, and the second charge knocks him down to the ground. When Astrid mentions that he was struck twice, Walter realizes that repetition is the key and heads back to the lab.
At the hospital, Peter wakes up on his own. He removes the monitor leads, gets dressed, and walks down the hallway, but has no memory of who he is. The hospital staff is preoccupied with the lightning victims, but one nurse starts to question him. She's called away temporarily and Peter goes outside and looks across Boston, which is in the middle of another dry lightning storm.
Peter walks down the streets of Pittsfield and hails a cab. He asks the driver to take him to an address in New York and gives him his credit card to cover the expense.
Sam takes Olivia to a museum which is in the middle of a storm. They talk to the museum curator, Dr. Christine Albright, and confirm that the key is in the Native American Wing. Albright advises them not to go in, since lightning strikes are occurring inside of the buildings, but Olivia says they have no choice.
Astrid provides Walter with the data on all lightning strikes, and Walter starts tracking the frequency of multiple strikes. Once he compares that to the frequency of other events, they can determine the cause. Once they overlay all of the activity, they find two foci with a rift between them. One foci is the hangar with the Machine, and the other is at Liberty Island. Walter realizes that it's where his counterpart is located on the Other Side. He goes to Broyles and uses two magnets to demonstrate how the two Machines are interacting. Walter suggests that they move their Machine to the same spot as the other one, slowing the rate of destruction until Olivia can find a way to get Peter into the Machine.
Sam and Olivia get to the Native American Wing and he prepares to break open a case with a tablet. Lightning strikes from the ceiling, setting off the security systems. The gate starts to come down and Sam blocks it with a well-rolled piece of debris that knocks over an urn, holding the gate open. Outside, he removes the key from the tablet. However, Sam doesn't know what to do and there's no hole for the key in the box. As Olivia handles it, it opens on its own. Inside is a piece of paper, and on it is the drawing of Peter in the Machine... and an additional drawing of Olivia.
At the lab, Walter examines the drawing and speculates that Olivia must have the ability to turn off the force field. He reminds her that she used telekinesis two years ago, and proposes that she can use it with her ability to jump between dimensions to manipulate the Machine on the Other Side and shut it down. When Olivia points out that she's had no experience, Walter remembers the typewriter that Fauxlivia used and sets it up. He then has Olivia concentrate and try to activate the typewriter on the Other Side.
The hospital staff that Peter has disappeared, and left a note saying that he's going home.
Olivia has no luck with the typewriter and suggests that Walter give her cortexiphan, but he warns that she's too old and needs to harness her abilities on her own. Walter tells her that he's accepted his own unique mind, broken as it may be, and encourages her to embrace the peculiar parts of her own mind. Olivia warns that believing it doesn't make it true, but he asks her to try. Nothing happens and he tells her to take a break. Astrid arrives to tell them that Peter is missing.
Broyles and his people are transporting the Machine to Liberty Island, while Peter wanders the streets and asks for help. He finally finds a man who directs him to a pawnshop. Peter goes inside and asks the manager for his collection of rare coins. After a moment's consideration, Peter picks out a silver half dollar and says that it's his favorite because it always brings him luck.
Astrid checks the Bishop house, and Walter worries that his son may be suffering from serious brain damage. He snaps at her and then apologizes, and Olivia tells them that she's traced Peter's two credit card purchases that place him in New York.
Peter arrives at Liberty Island as the authorities evacuate the island. The guard orders him to leave with the others, but Peter says his father is Walter Bishop... the Secretary of Defense.
In the lab, Sam worries that the intervened. Broyles arrives to tell them that Peter has turned up at Liberty Island. They prepare to leave, and Broyles tells Sam that they'll only be taking official personnel. Sam wishes Olivia luck and then goes to the shore and uses his executive toy to monitor the vibrations.
Walter and Olivia greet Peter, who starts to realize that he's been having memories of the Other Side. Walter checks him and confirms that he's starting to recover his memories. He notices the silver half dollar, but before he can pursue the matter, Liberty Island starts to shake. Walter warns Broyles that the system wasn't designed to compensate for the fluctuations. Meanwhile, Olivia explains Walter's theory to Peter, and says that she's been concentrating on the phrase that Walter gave her.
At the lab, Astrid hears the typewriter moving on its own. She investigates and then calls Olivia and tells her it's sending a message: "Be a better man than your father."
The microquakes increase and Broyles evacuates all non-essential personnel. Walter warns that they don't have much time, and assures Olivia that whoever sketched the drawing believes as Walter does that Olivia doesn't fail. Peter studies the Machine and Olivia comes over. They both admit that they're not ready and then move forward. Olivia concentrates and shuts down the Machine on the Other Side, and their Machine's force field deactivates.
On the Other Side, Brandon realizes what has happened and notifies Walternate.
As Peter starts to enter the Machine, Olivia tells him that she loves him. They kiss and then Peter steps into the Machine. The clamps fasten around him and there's a surge of power...
...and Peter finds himself on a street at night. There are flames everywhere and people are running in terror. Peter looks around and sees a memorial to the Twin Towers... which fell on September 11, 2001. The memorial was dedicated in September 2021. Soldiers order everyone off the streets and a Fringe Division agent comes over to Peter. He knows who Peter is and points out that he's wounded, and Peter starts to pass out from the injury.
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