Olivia wakes up from a dream where she sees herself and Peter making love. Her phone is ringing, and she answers to confirm that it’s Peter, calling to let her know that he and Walter have had a breakthrough at the lab and need her help. When she arrives, Peter explains that they’ve constructed a biomechanical interface that allows Peter to interact with the Machine. However, they need to get access to the Machine to test their device, and they need Olivia to get Broyles to authorize access.
A truck driver is passing through Southern Vermont when first his radio and then his engine goes out. He gets out and discovers that several other people have had similar problems. They see a lights and hear a roaring noise, and watch as a jet passes overhead and crashes a mile behind them. As they stare in horror, all of their car engines and radios come back on.
The next day, Broyles, Olivia, and Astrid arrive at the scene and have confirmed that the jet’s electrical systems went out, causing the plane to crash. Astrid is trying to raise Walter is on the radio and is surprised when Peter arrives with Walter. As Walter examines the car, Olivia admits that she’s pleased that Walter has been loosening up recently. Walter confirms that the cars were magnetized due to a strong electromagnetic pulse, and then decides that he wants some rhubarb pie and saw it on sale at a diner in the nearby town of Westfield.
As Walter, Peter, and Olivia drive into Westfield, Olivia discovers that she can’t get a signal on her phone. While she goes to the payphone to call Broyles, Peter and Walter go to the diner. The cook, Willy, assumes that Walter is joking when he says that he just got out of a mental institution and doesn’t know how to drive. He offers Walter the pie on the house and goes to get a piece for him. Meanwhile, Olivia finds the early evening streets deserted and finds a car that has been abandoned with its doors open and its lights on. She tries to call Astrid but discovers that the landlines are also dead.
Peter goes to the restroom and when he comes out, hears someone groaning. Meanwhile, Willy comes over to Walter but doesn’t remember the conversation that they just had. When Walter reminds him that he offered to get him pie on the house, Willy turns violent and accuses him of stealing food. He says that he won’t even let Cliff steal food, but then smiles, recognizes Walter, says that he’ll get him his free pie, and goes to get it.
Peter discover that there’s a wounded man in a storage closet, bleeding. Meanwhile, Willy suddenly grabs a knife and attacks Walter. Peter arrives in time to pull him off and Olivia comes back and shoots the cook. Walter checks the man and discovers that his eyes each have two pupils. He then examines the wounded man and discovers that he’s been badly wounded. Olivia finds a dead body behind the counter, and Walter insists that they have to get the wounded man to a hospital, and it’s 20 miles away. As they drive out of Westfield, the man wakes up and says that his name is Cliff Hayes. He tries to warn them that they can’t go to the hospital as they pass the “Leaving Westfield” sign. However, a minute later they come to the “Welcome to Westfield” sign. Olivia is sure that they can’t have gotten turned around and keeps driving out of town, only to come back to the welcome sign. Cliff tells them that they can’t leave and the trio realizes that they’re trapped.
Back in Westfield, Olivia and the others take Cliff to the sheriff’s office but find no one there. Walter has Peter get a first aid kit and works on Cliff. When Cliff recovers, he tells them that the town isn’t safe because everyone in town has gone crazy. It started three nights ago when his sister shot a man who broke into her house. However, it was her own husband, but she had no memory of him even though they had been married for 18 years. Cliff’s sister then started talking about people she’d never met and things that she’d never done. Walter suggests that she might be suffering from something similar to schizophrenia. The amnesia spread to many of the other townspeople as if it were a disease, all of who became violent. However, Walter points out that a disease wouldn’t account for their inability to leave town. Cliff tells them that several people were immune and took refuge in the local hospital, including his wife Angela and daughter Lacey.
Peter suggests they find a power source to boost their radio signal and a high point, and Cliff says that they have a generator at the high school. Olivia wonders if the nearby military base is responsible, like the case they handled in Edina, but Walter says they never had such a case. Peter remembers that it’s a case from his timeline, but Olivia says that she must have read about it in his debriefing file.
As the new day arrives, everyone arms themselves and head for the high school. A man comes toward them, carrying a bloody doll and oblivious to their presence. Olivia is unable to start the car even though it worked earlier, and Walter warns them that the electromagnetic effect is intermittent and they can’t wait for the next lapse. As they head for the high school, Olivia complains about tremors and dizziness and then starts slurring her words. Peter goes to her side and she explains that for a moment it seemed like someone else was in her head. She gives Peter her gun, worried that she’ll go berserk and shoot someone just as the others did.
At the high school, another of the immune townspeople, Brian, lets them in. He warns them that one of the seemingly immune people, Teresa, became “infected” earlier that morning, and then complains that the government isn’t helping them. Angela and Lacey come to greet Cliff, while Walters goes to the biology lab where the others are keeping Teresa. She seems to have no idea what is going on and alternates between two different sets of memories, one where her husband died seven years ago and one where he’s still alive. Walter examines her and discovers that she has two sets of teeth.
Peter arrives to tell Olivia that he still couldn’t get a signal through. He suggests that Walter test Olivia as well and he reluctantly agrees. As they wait, Olivia comments on how Walter appears to be socializing again since he started working with Peter. They talk about Peter’s Olivia and he says that always saw the best in people, and that she gave him a place that he could call home. Peter also mentions an Italian restaurant that they used to order out from. They hear a scream and run to investigate. The survivors have found Teresa, dead of self-inflicted wounds. As Cliff worries about what will happen to his family, he mentions that he only lives in Westfield because he couldn’t bear to take a job and move away from home. However, Olivia assures him that the others might be dead if he wasn’t there for him.
Walter finishes his testing and tells Peter and Olivia that he found twice the normal amount of genetic material in Teresa’s blood. He speculates that someone is merging the two universes at Westfield, just as he and Bell managed to do on a much smaller scale. Due to the overlap, no one can escape the town. Meanwhile, people are merging with their doppelgangers from the Other Side and going insane because they are unable to distinguish between what is and isn’t real. When Olivia wonders if they can be helped, Walter admits that the damage has been done and there is no w ay to reverse it. He absent-mindedly tells Olivia that her own blood tested clean, much to her relief. They realize that the people at the high school are immune because they have no doppelgangers at the Westfield on the Other Side. Peter wonders how it could be done and Walter admits that there is no such power source. However, Peter points out that David Robert Jones was using amphilocite and it could generate enough power. Walter realizes that they could do it with that mineral, and warns them that what they’ve seen so far is only phase one. The building shakes and Cliff calls them out to the roof. They go out and see the town beginning to disintegrate, and Walter tells them that’s phase two.
Cliff goes downstairs to make sure that Angela and Lacey are okay, while Walter admits to Peter and Olivia that he has no idea what to do. The two towns are merging and disintegrating since two objects can’t occupy the same space simultaneously. When he starts to panic, Olivia tells Peter to calm Walter down. Peter suggests that they can use an opposing force to negate the merger, and Walter suggests that they find the center of the merger, the safest spot. They prepare to move out and Olivia has Peter find any older vehicles without fuel-injected engines. Brian tells them that he has a better idea, while Peter and Walter work together to find the exact center of the confluence.
Brian drives up an older school bus and they load everyone on board. As they drive down the street, Walter notices that Lacey is nervous and assures the girl that everything is okay. However, she screams when she sees some of the passengers, who has manifested a second face because of rapid-onslaught DNA multiplication. Peter struggles with the man until Olivia shoots him, and they dump him out the back.
The group drives through the disintegrating town until they’re forced to walk when the road ahead is block. They get to the bike shop at the center of the merge and take refuge inside. The two towns combine and disintegrate. Once the chaos dies down, the survivors come out and discover that the town of Westfield has been rendered into ash.
The FBI and medical teams arrive and confirm that only the small group survived the merger. Broyles tells Olivia that they found several amphilocite-powered devices on the outskirts of the town. However, they have no idea what David Robert Jones was trying to accomplish. Olivia goes over to Cliff, who assures her that Lacey is fine. The FBI agent assures him that the Bureau will provide temporary housing, and Cliff says that as long as he has his family and they’re safe, then they’ll be fine.
That night, Walter and Peter go back to the lab. Walter wants Peter to stay, a total turnaround from his initial reaction, but Peter says that he has to go home. However, he stops at Olivia’s apartment, stopping by to check on her. Olivia tells him that she ordered Italian food from the local place that Peter mentioned earlier and then kisses him.