In New York City, EMTs bring in an injured Nina Sharp. They reveal that her artificial arm has a hole in it. At FBI headquarters, Olivia gets word of the attack. Broyles runs the security footage and they see men come in, shoot the night guard, replace him, and then go upstairs to wait for Nina. Once she arrives, they shoot her and a man wearing bandages blacks out the camera for four minutes. Olivia has the tech enhance the audio and then run the bandaged man's voice through software recognition. They identify him as David Robert Jones. Olivia wonders why Jones would shoot Nina if he works with Bell. She insists on bringing in Bell, and Broyles finally manages to tell her he's already ordered Bell brought in. They get a call that Nina is out of surgery.
Peter arrives at the lab to discover that Walter has disappeared and Astrid has no idea where he is. Olivia arrives to talk to Walter and Peter notes she doesn't look well. She brings him up to speed on Nina's shooting, and then wonders if Walter left because she blamed him for the Cortexiphan trials. Peter says that Walter understood why she came after him.
Walter is at a cemetery looking at a tombstone. The Observer watches him from a short distance away.
Broyles goes to see Nina as she wakes up. She checks her injured arm and Broyles asks what Jones wanted. Nina asks to speak to Olivia right away. Olivia arrives while a Massive Dynamic team repairs Nina's arm. Once they're done, Nina insists that Bell has nothing to do with ZFT. Jones was one of Massive Dynamic's first employees, was fired, and felt spurned by Bell. She believes that Jones is trying to prove something to Bell because no one recognized he was special. Nina hasn't seen Jones in years, but he contacted Massive Dynamic to request a meeting with Bell. Nina never told the FBI because they considered it a private matter. She believes that Jones plans to kill Bell. When Olivia insists they put Bell in protective custody, Nina says that she hasn't seen Bell in months and he has been communicating electronically with her. She offers Olivia a deal: if Olivia stops Jones, she'll set up a meeting with Bell. Olivia demands to know what Jones did to her in the elevator, and Nina reveals that Bell hid a powerful energy cell in her arm.
Jones and his team park in a New York City street and set up electronic equipment in the middle of the road. They activate the equipment, which causes a high-pitched noise that the bypassers notice. A glowing gateway opens in the middle of the street and a truck starts to drive through it. Jones' men lose the coordinates and the gateway closes, cutting the truck in half. It crashes to a half and Jones declares the area too thick so they need to move on.
Walter and the Observer are walking on a beach. They stop and the Observer asks Walter if he recognizes a coin. Walter does, and the Observer explains the coin is similar to the one he's thinking of but it's from a different place. He tells Walter "There is more than one of everything," then admits he's said too much and isn't supposed to get involved. He asks if Walter remembers what he has to find at the beach house that they've arrived at. When Walter admits he doesn't, the Observer says he must and warns there isn't much time.
Broyles and Nina go to the Harvard lab and ask after Walter. Peter comes in and they admit that Jones has stolen something Walter may have knowledge of. While Nina orders a grid search, Charlie and Olivia investigate the truck. The witnesses describe the gateway and the fact a man with a machine was present, and he wore bandages.
Nina's people turn up Walter's image on a Massive Dynamic security monitor at a commuter train station. Peter recognizes the location as near to a beach house that Walter went to for calm. Peter insists on going to get Walter.
Olivia and Charlie go over the report of the driver, who died in the accident, and the ID from the truck. None of the engine parts show up in any file, nor do the driver's fingerprints.
Peter arrives at the beach house and finds Walter inside. Walter is holding the coin and insists what he's looking for is in the house.
At FBI Headquarters, Olivia demands answers as to Bell's location. Nina finally admits that Bell is in a different world.
Jones' team travels to a soccer field in Providence, Rhode Island. Meanwhile, Olivia tries to explain the concept of parallel worlds to Charlie, and the fact that some people can travel from one world to another. Jones plans to use the energy cell to cross over and get to Bell. They're interrupted when they get a call from the soccer field.
Walter desperately searches through the house, saying he started something a long ago and he has to finish it. Peter remembers how he and his mom came down to the beach house when Walter was working in the city. Then he'd smell pancakes on Saturdays and realize Walter was there. Walter remembers he made them in the shape of whales and knows where what he's looking for is.
At the soccer field, Charlie and Olivia talk to a witness who reports an odd gateway appeared and one player ran into it by accident. They check the corpse of the player, which was partially disintegrated when the window closed. The agents wonder what the two locations have in common. Back at headquarters, Olivia has agents assemble files on all reported paranormal activities. She marks all of the incidents on a map and realizes there's a pattern.
Walter finds a trunk with a metal box… and the coin on top of it. The box is locked and Peter goes to work on it. He gets it open and Walter removes a handheld device. He explains that he and Bell took LSD and saw what they believed was a parallel world with slightly different variations of the people in their world. They tried to create a way to travel to the other world, and Bell believed they could use Cortexiphan to alter subjects to travel to the alternate world. Walter lost something precious at that time and tried to find a way to go to the alternate world to replace it. However, it's not that easy. Also, Walter created a "plug" device to close a window as necessary, and he knows that there's a major soft spot at Reiden Lake.
Olivia shows Nina and Broyles the map of occurrences and the fact that many of the spottings originate. Nina explains Bell's theory that there are "soft spots" where the universal constants begin to decay. In those areas, the membrane between realities is thinner. As Mankind has accelerated its technological advances, the decay has hastened. She warns that if Jones can find the necessary spot and focuses the necessary energy, he can create a window to another reality. They check the oldest events and determine they're centered around Reiden Lake.
Peter drives Walter to Reiden Lake, and Walter says that his friend said he needed to get there. Peter realizes he's talking about the Observer and Walter insists the Observer is on their side. They come to a chain barricade and Walter takes out the plug device. He then shows Peter a coin and says that when Peter was little and sick, he collected coins. The one Walter has is his favorite, but Peter admits he doesn't remember anything of that. Suddenly men yank them out of the car, but Olivia arrives to call off her FBI agents. They see a flash of light up ahead and go to investigate.
Jones and his men are beginning to open a window at the lake. Jones' men spot the FBI and open fire, and Jones tells his people to hold off the FBI. Charlie covers Olivia as she goes in, and Peter insists on using the plug device to seal the window so Walter doesn't have to. Olivia tells Jones and his assistant to stop. When they refuse, she shoots the assistant. Jones finishes stabilizing the portal and prepares to enter the window. Olivia shoots him but he's only staggered. Jones explains that the teleporter has made him partially insubstantial. Jones enters the window but Peter uses the device to close it… with Jones halfway through. What's left of his body falls to the ground.
Back in her office, Olivia receives word from Broyles that their superiors have shut down any investigation into Bell.
Astrid and Peter arrive at the lab and find a note from Walter saying that he's going out for a while but he knows where he's going. When Astrid wonders if they should call the police, Peter says it's the first time Walter has left a note and figures he's fine.
Walter goes back to the cemetery and puts the coin on top of a tombstone: one with the name Peter Bishop, 1978-1985.
Olivia receives a call from Nina saying she is going to uphold her end of their bargain. She tells Olivia to go to a hotel in Manhattan and wait for her. Nina tells Olivia not to say anything to anyone and to come alone.
Olivia goes to the hotel and waits for Nina. She finally calls and discovers that Nina is out of the country. She takes the elevator down but the lights flicker and other people appear and then disappear around her. The doors open to reveal a white corridor. A woman is clearly expecting her and leads Olivia to an office. Inside is an oxygen tank and a newspaper talking about the President moving into the new White House. A man comes into the room and introduces himself as William Bell. Olivia goes to the window and looks out from one of the twin towers of the World Trade Center.