New York. A gunshot victim is urgently wheeled into the hospital emergency room. One of the medics points out to the ER doctor that the gunshot wound isn't the victim's only injury. The victim is Nina Sharp, and her bionic arm has been torn open.
At the FBI, Broyles and Olivia discuss Nina's condition. Charlie shows them video surveillance from the attack at Nina's apartment building. A man wearing bandages on his face enters, kills the security guard, then shoots Nina as she is about to exit the elevator. As the man opens a briefcase full of bizarre surgical devices, he says something inaudible to one of his cronies. An FBI tech runs a voice recognition program on the man's voice and gets a match: David Robert Jones.
Olivia wonders why Jones is wearing bandages. As it stands, it appears as though Jones is working for William Bell. She's determined to bring Bell in for questioning. Broyles receives a call informing him Nina Sharp is out of surgery.
At the Harvard lab, Peter and Astrid realize that Walter is missing. They are making phone calls to find him when Olivia arrives, also needing to speak with Walter.
Walter is walking through a cemetery. He comes to a gravestone and stops, deep in thought. Several yards away, the OBSERVER stands and watches him.
David Robert Jones and his men arrive at a busy intersection in New York City and begin setting up some peculiar equipment in the middle of the road. Jones's face is partially covered in bandages, and the visible parts of his skin have ugly yellow lesions.
Olivia visits Nina, who is being worked on by a team of Massive Dynamic medical technicians. When they are finished, Nina reiterates to Olivia that William Bell is not the problem. She says Jones used to work for Bell, but he was let go a number of years ago. Jones considered Bell a mentor and felt snubbed. She believes that Jones is intent on finding and killing Bell. Nina tells Olivia that if she stops Jones, she will arrange a meeting between Olivia and Bell. But if Jones succeeds, all of the answers Olivia needs will die with Bell. Nina also reveals that Jones stole a very advanced energy cell from her bionic arm.
Back at the intersection, Jones places the energy cell he stole from Nina into the mysterious device and powers it up. The device emits a wall of sound, and then a shimmering window appears in the middle of the intersection. In the window is the exact same street, but with small differences -- almost as though it's a glimpse of the same street at a different time. Jones waits for the window to stabilize as a big rig truck heads straight for them. As the truck passes through the window, the window closes around the the truck, splitting it in half and setting it on fire. As pedestrians and cars swerve to avoid the fiery mess, Jones commands his men to do it again and get it right.
Somewhere on a beach, Walter and the Observer stand looking at a beach house. The Observer gives Walter a coin, which Walter appears to recognize. But the Observer explains that this isn't the coin he's thinking of; it's from another place. There is more than one of everything, he says. The Observer asks if Walter knows what he needs to find, but Walter can't remember.
Broyles brings Nina to the lab to talk with Walter. When they discover Walter is missing, both Broyles and Nina begin mobilizing their resources to search for him.
At the intersection, Charlie and Olivia question witnesses who tell them about the window and how the truck came out of nowhere. One of the witnesses says the man operating the device was wearing bandages.
Nina receives a surveillance photo of Walter stepping off a train in Grafton. Peter says his family used to own a beach house nearby that Walter was particularly fond of. Peter says he'll go fetch Walter himself.
Charlie and Olivia receive an update. The driver doesn't have any prints and the truck isn't registered anywhere. Moreover, the VIN number and serial numbers for parts don't exist. This truck was never made.
Peter arrives at the beach house and finds Walter upstairs, visibly upset and searching for something.
At the FBI, Olivia tells Nina and Broyles about the truck. Olivia reiterates her demand to meet with William Bell, saying she will turn the world over to find him. But Nina replies that Bell is not, in fact, in "this world."
A park in Providence, Rhode Island. A group of kids are playing soccer when Jones and his team arrive.
At the FBI, Olivia explains the concept of multiple realities ("The Road Not Taken") and how it's possible that Bell is living in another universe. The window Jones opened at the intersection was a glimpse into this other universe. Nina suspects Jones is trying to cross over so he can find Bell. Just then, they get a phone call saying another event has occurred.
Back at the beach house, Walter ransacks a room, still searching. He is becoming increasingly agitated. To help calm Walter down, Peter begins to reminisce about their days at the beach house. He describes how Walter used to make pancakes for him, in the shape of whales. Walter listens, enjoying this moment of nostalgia -- and suddenly he remembers why he's at the beach house, and what he is looking for.
Olivia and Peter arrive at the soccer field, now a crime scene, and begin to interview people. Their descriptions match those of witnesses from the intersection: they saw a shimmering window that seemed to reveal the same park, yet slightly different. Olivia wonders why Jones chose these two places.
At the FBI, Olivia creates a map of all Pattern events in the Northeast corridor. As she finishes plotting these events, she has a revelation.
Walter finds an old box in a closet. On its top is a coin much like the one the observer gave him. He pockets the coin and hands the box to Peter.
Olivia explains her theory to Nina and Broyles. Using a computer, she shows how numerous Pattern events seem to radiate outward from the intersection. And a number of other Pattern events radiate outward from the soccer field.
Peter picks the lock of the box and Walter removes a device. He explains that when he and William Bell used to do LSD, they believed they were glimpsing other realities and set out to recreate that sensation without the hallucinogen. Bell believed that children could do this naturally, but socialization removed that ability. So Bell invented Cortexiphan, which, in theory, would preserve and amplify the ability. Around the same time, Walter says he lost something he was very fond of. So he built a device to cross over to another reality, so he could steal the duplicate of the thing he'd lost and take it back with him. But, Walter says, you can't just cross over anywhere; it has to be done in the right place.
At the FBI, Nina explains that there are "soft spots" in the world -- places where the fundamental laws of physics are deteriorating, partly as a result of human technological progress. If Jones successfully deploys the device in one of these soft spots, he could potentially cross over.
Walter tells Peter that if a door were opened between realities, things from "there" could potentially pass over "here." So Walter built a plug to patch one of these holes. This plug is what was in the box. And Walter also knows where they need to go to use it.
Back at the FBI, Olivia is still piecing the Pattern sightings together. Not all of the events are accounted for by the radiating patterns from the intersection and park. She highlights the oldest Pattern events, and sees that these events all radiate outward from a third location: Reiden Lake.
Peter and Walter drive the station wagon to a spot in the woods near Reiden Lake. Walter shows Peter a coin. He tells Peter that when he was young, he became sick, and he took to collecting coins as a way of coping. The one in his hand was Peter's favorite. But Peter says he doesn't remember any of this. Without warning, men in black pull Peter and Walter from the car -- but it turns out the men are FBI. Olivia tells the team to let them go. Off in the distance, they hear a noise and see a bright light filtering through the trees.
Jones and his men have already set up their device, and they have successfully opened up the window. A shimmering window shows an alternate view of the lake, where it appears to be raining even though the sky above the window is clear. A gunfight ensues between the FBI and Jones's men. Meanwhile, Walter tells Peter he needs to point the plug at the window and press a button to make the window close.
Olivia creeps up behind Jones as the gunfight continues. She orders him to stop, but he ignores her and finally stabilizes the window. She shoots him. Once. Twice. But Jones, still standing, tells Olivia that the aftereffects of his teleportation ("Safe" and "Ability") may eventually kill him, but until then they have made him very special.
Jones nears the window and prepares to cross over. Olivia runs to stop him. Peter is close behind with the plug. Jones pushes his way halfway through the window. Peter presses the button on the plug -- and the window snaps shut on Jones, slicing him in half.
Later at the FBI, Olivia packs files from her office into a box. Broyles interrupts and tells her that they've received orders from the top to cease their investigation into William Bell.
At the Harvard Lab, Peter and Astrid find a note from Walter saying that he is going out for a while, but not to worry, he will be back.
Walter walks back through the cemetery. He stops in front of the same gravestone as before. He withdraws the coin from his pocket, his eyes now wet with tears. He places the coin on the top of the grave, which reads:
In her apartment, Olivia locks her gun and badge away. She gets a call from Nina asking if she can meet her at the Matsumi Hotel in Manhattan for breakfast the next day. Olivia kept up her end of the bargain by stopping Jones, so Nina will now arrange a meeting with William Bell.
Olivia drives into New York. As she enters the city a car suddenly pulls out in front of her -- but she swerves and narrowly avoids a collision.
Olivia waits in the hotel dining room for Nina. After what seems like many hours, the dinning room is completely clear of patrons. Olivia, irritated, calls Nina's office asking to speak with Ms. Sharp. Nina's office informs her that Nina is out of the country.
Olivia leaves the dining room, boards an empty elevator, and presses DOWN. As it descends, there is a flicker, and Olivia gets a quick glimpse of people all around her in the elevator. But the effect subsides, and Olivia is again alone.
The elevator door opens to reveal a white hallway. She is greeted by a WOMAN who leads her into a cozy office. Olivia takes in the office's details, notably a newspaper on the coffee table whose headline says that President Obama's family will soon move into the "new White House."
A man enters the room. He tells her he's been waiting a very long time for this. Olivia wants to know where she is and who he is. As the man steps out of the shadows to reveal his craggy face, he says the answer to her first question is complicated, but the answer to her second is... that he is William Bell.
Olivia turns toward the window, admiring the top floor view of the New York skyline. But something is off; this view should not be possible. Olivia stands there perplexed, as we pull back to see that she is inside one tower of the still-standing World Trade Center.