Olivia dreams of her and Peter making love. She wakes up when Peter calls to tell her that he and Walter have had a breakthrough on the machine. However, they need her help. She arrives at the Harvard lab where Walter is creating a breakfast cocktail. They explain that they've completed the biomechanical interface to the Machine, and it will only respond to Peter's DNA. Peter demonstrates and they explain that they need Broyles' authorization to get them to test it on the Machine. Olivia says that she'll do what she can.
In Southern Vermont, a trucker is driving along the road when his radio goes out. His engine shuts off and he pulls over, and stares as the items in his cab briefly float into the air. There are other people on the road and they all gather as a bright light shines overhead. It comes down and they realize that it's a jetliner. They watch as it crashes nearby. After a second, all of their cars start up.
The Fringe team is called in and Broyles explains that the jetliner's hydraulic and electronic systems failed and they crashed. Astrid is unable to raise Walter on the radio, and is surprised when Walter comes up behind them with Peter. As he goes to check out the site, Olivia notes that Walter has loosen up recently. Walter confirms that the cars are magnetized because the electromagnetic force in the area increased. While they work, Walter suggests that Peter go get some rhubarb pie.
The trio drives to the diner and Olivia discovers that she can't get a signal. She goes to the payphone while Peter and Walter go into the diner. They chat with the cook, who is surprised when Walter explains that he hasn't renewed his license since he got out of the mental institution. The cook, Willy, assumes that Walter is joking and gives him the pie on the house.
As Olivia walks down the street, she notices a car with the doors open. She tries to call Astrid but discovers that the line is down.
Peter leaves the restroom and hears someone groaning.
Willy comes over to talk to Walter and acts as if he hasn't talked to him, and asks what his order is. Walter insists that he ordered and says that he offered him the pie on the house. Willy owner gets angry at him, insisting that nobody steals from him, not even Cliff. After a moment, Willy becomes much friendlier, says he'll get Walter the free pie, and walks away.
Peter follows the groaning noise and finds a man bleeding in a store room.
Walter nervously watches Willy as the man gets him his pie. However, the cook then grabs a knife and attacks Walter. Peter runs in and struggles with the owner, and Olivia arrives to shoot the man. Walter checks Willy's eye and determines that it has two pupils. He then checks on the man in the storeroom and confirms that he's in bad shape, while Olivia finds a dead body beneath the counter. Walter warns that they can't treat the man with medical equipment, and the nearest hospital is 20 miles away. They drive out of Westfield and the injured man wakes up. He insists that they can't go to the hospital, and says that his name is Cliff Hayes.
The car passes a "Leaving Westfield" sign and Olivia continues, driving past the departure sign. However, they come to another welcome sign a few seconds later. Cliff mutters that they can't leave, and Walter realizes that they're trapped.
The trio goes to the sheriff's office but finds the building seemingly abandoned. The phone lines are still dead and Walter tells Peter to find a first aid kit. As he works, Walter explains that he saw a similar phenomenon before in Brigadoon, the musical. Cliff tells them that they're not safe and that everyone in Westfield has gone crazy. He tells them that three nights ago his sister said that a man broken into her house. He got no answer from the sheriff, went over, and found his sister's husband shot in the head. However, it turned out that his sister shot her husband, and claimed that she'd never seen him before in her life even though they'd been married for 18 years. The sister was talking about people she'd never met and things that she never did. Walter notes that the symptoms are similar to those of schizophrenia. The illness soon spread, and Walter notes that an illness doesn't account for their inability to leave town. Cliff continues, explaining that in each case the people had amnesia and then turned violent. A few of them are immune and holed up at the high school, including Cliff's wife and daughter.
Peter needs a booster for the radio and a higher spot to try and call Broyles. Cliff says that there is a generator at the high school, while Olivia suggests that the military might be responsible, like the case they handled in Edina. Walter doesn't remember the case, but Peter notes that he had a case in Edina with his Olivia and Walter. Olivia dismisses it, saying that she must have read it in Peter's debrief. Walter asks for one of the rifles but Peter gives him pepper spray.
As the sun rises, Olivia gives a gun to Cliff, who admits that as a teacher he's never shot one. They head for the high school to get to the generator. They hear someone humming and see a man come toward them, holding a bloody doll. He ignores them and keeps walking, but Olivia is unable to start a car. Walter says that the electromagnetic effect is intermittent and they don't know how long they have until it fades away. As they walk, Cliff comments that he can see the resemblance between Walter and Peter. Meanwhile, Olivia complains about tremors and dizziness, and then starts slurring her words. She then tells Peter that it felt like someone else was in her head. Olivia gives Peter her gun, worried that the same thing that affected the others is getting to her as well.
The group gets to the high school and one of the immune townspeople, Brian, lets them in. They explain that 12 of the made it, but Brian says that one of them went insane that morning. Cliff's wife and daughter arrive and embrace Cliff. Peter tells Olivia that they should tell Walter what's happening to her, while Brian angrily demands to know what the U.S. government is doing. Olivia insists that they need to work together to get out, and Walter asks to see the affected woman, Teresa. He examines her and she wavers in and out of consciousness. Walter checks his teeth and discovers that she has two sets of teeth. He tells Olivia that the cook at the diner had two irises and suggests that something may be causing rapid mitosis. Teresa talks about her husband, Lee, who died seven years ago. However, Teresa insists that she talked to Lee that morning. When Walter asks her about Lee, she snaps at him, insisting that Lee has been dead for seven years. However, she then reverts to talking about Lee as if he's alive.
Peter comes in and says that even with the generator, he couldn't get a signal through. Olivia tells him about Teresa and Peter suggests that Olivia let Walter test her as well. Walter checks her but dismisses them as psychosomatic. As he goes to run the tests, Olivia tells Peter about how Walter has improved so much since Peter has arrived. She then asks about Peter's Olivia and he tells her about how she sees the best in people and gave him a place to call home. As they talk, they hear a scream and run to the restroom. Teresa got loose and cut her wrists. Cliff wonders why nobody has come and how the disease could have affected Teresa. He comments that he wasn't supposed to be there, and that he was offered a job but didn't take it despite his wife Angela's insistence. Olivia notes that the others might not have made it without him.
Walter calls Olivia and Peter to the biology lab and explains that he found twice the normal genetic material in Teresa's blood. He explains that he and Bell managed to overlap the two realities in a goldfish bowl, and believes that the two universes have merged together at Westfield. The three of them are trapped in the overlap, and the people are merging with their doppelgangers from the Other Side. Their minds are unable to distinguish what is real and what isn't. Walter warns that the damage is done, but finally tells them that Olivia's blood is fine. He then explains that the others at the high school are okay because they don't have doppelgangers in the other universe. On the Other Side, Cliff took the job and left town. Walter says that he can't imagine an energy source that could merge two worlds, but Peter suggests that David Robert Jones was mining amphilocite to generate enough power. Walter admits that it's possible, but warns that the effects he's described are only phase one.
The building shakes and Cliff comes in to tell them there's something they need to see. He takes them to the roof where they can see that buildings are disintegrating: phase two.
Back in the school, Cliff calls his daughter Lacey away from the window as the building continues to shake. Walter admits that he has no idea what to do. With the two towns merging together, the fundamental forces of physics are colliding, upsetting the balance because two things can't occupy the same space at the same time. Walter panics and Olivia suggests that Peter should talk to him and calm him down. Peter goes over and suggests that they can offset the two worlds with an opposing force. Walter realizes that they need to find the eye of the storm, the true center of the merger. Olivia asks Cliff to find any older vehicles without fuel-injected engines, but Brian has a better idea.
Peter and Walter triangulate their entries points and the buildings that Cliff has said have been destroyed. Together they determine the center of the merger, Cypress and Quimby, four miles from the school. Brian arrives with a school bus and everyone gets aboard. They drive to the bike shop at the address while Walter tries to reassure Lacey. However, she screams when one of the passengers merges with his other self, growing two faces. He goes berserk and Walter stuns him with the pepper spray long enough for Olivia to shoot him. Peter dumps the man out the back and they get moving.
Brian drives the bus until they come to a telephone pole blocking the road. They continue on foot as the bus disappears into the merger. Everyone gets into the bike shop and the window shatter as the two towns combine. A few minutes later, the chaos dies down and the group looks outside: every building in the town has disappeared.
Broyles arrives with the emergency teams and they confirm that there are no other survivors. He tells Olivia that they found several amphilocite devices planted around the town, and they wonder what David Robert Jones hoped to accomplish. Olivia goes over to Cliff, who is surveying the devastation, and he assures Olivia that Lacey is fine. He wonders how everything he has known could have disappeared, and Olivia assures him that the FBI will provide him with temporary housing. Cliff assures her that he has his family and they'll be fine.
Back at the lab, Peter is preparing to leave but Walter says that he was making dinner. Peter assures him that he'll be back in the morning and hopes that Broyles will give them permission to use the machine. Walter wishes Peter good night and goes back to work.
Olivia is at home preparing for bed when there's a knock at her door. It's Peter, who says he was in the neighborhood and wanted to check on her. She tells him that she ordered from their favorite restaurant and kisses him, much to Peter's surprise.