At a playground, Olivia is lying down on the ground and feels someone stroking her face. It's Peter, who tells her that she won't be getting rid of him that easily. He points out Walter, who is swinging on the swings, and they agree that it's the perfect day. As they agree, Olivia says that the day has to end and that he can't keep ignoring the problem. When Peter asks what's wrong, she says that he is the problem...
... and Peter wakes up in his holding room as Olivia comes in. She apologizes for waking him up and then says that they have a problem with time, and it's related to his appearance.
In Central Village in Boston, a mother, Anne, is working in the kitchen as her five-year-old daughter Samantha comes in. Anne looks around and sees that the kitchen has apparently been through a fire. She gets Samantha, now a one-year-old baby, and runs outside, and sees that the apartment has been through a fire... and then it reverts to normal as Anne's daughter becomes five years old again.
Olivia drives Peter to Massive Dynamic and explains that there have been several incidents involving time loops. He doesn't know what that means and Olivia explains that several similar effects occurred just before Peter arrived. When Peter wonders what Walter's theory is, Olivia explains that Walter has refused to consider the matter. They get a call about the incident in Central Valley and drive there, where Lincoln and Astrid are already examining the house. Olivia tells Peter to stay put and then talks to Broyles, who explains that a flash fire occurred. Meanwhile, Peter talks to Anne and Samantha and helps find a missing stuffed animal. Olivia calls him over as Lincoln confirms that the scorch marks made a perfect circular pattern and that there was a fire in the apartment four years ago. Broyles wants Peter taken to Harvard so that Walter can examine him, overriding Walter's objections.
Later, Walter examines Peter, calling him "the subject." He finishes the examination and tells Olivia that Peter isn't the source of the time anomalies, but Peter points out that Walter has no way to confirm that after such a brief examination. Walter ignores him and goes to his bedroom, and Olivia explains that Walter has lived exclusively in the laboratory since he was checked out of the institution three years ago. Peter goes to work, explaining that he thinks that when he returned, he damaged the time-space continuum. He believes that the anomalies will get worse.
That night, three teenagers are driving to a band when they abruptly brake to a halt as the image of a train crosses in front of them.
The next morning, Peter admits that he can't work things out because there are too many variants. Olivia reports that there have been at least 65 timeslips within 40 miles of downtown Boston. As she discusses the case with Peter, Walter comes in, ignores Peter, and makes a bologna sandwich. Olivia asks for his help and he says that he'll join them once his lab is back to him. Walter leaves and Olivia explains that Walter was having visions. Peter has no idea that he was appearing in the dreams of either Walter or Olivia, and Olivia wonders how it was possible. He ducks the question and says that the lab is home and suggests that they were seeing echoes of the other timeline. Lincoln comes in and gives them a report about the train incident. Peter grabs a Geiger count and starts to go with them... and finds himself at the site. The teenage driver, Dylan, is describing the incident and how the image of the train appeared spherical. As they drive back, they confirm that the train line was decommissioned four years ago. Peter is happy to hear that there's a pattern... and finds himself back at the site of the train appearance, arriving for the first time. He discovers that the teenager's truck has been rendered brittle...
... and finds himself back in the SUV driving back to Boston with Lincoln and Olivia. He explains that neutron radiation caused the brittle metal and that it doesn't occur in nature, meaning that someone is causing the time events.
Kate Green is working at home, scribbling on a blackboard, when her husband Raymond comes in. He tells her that after 30 years, he's turned over a new leaf and she doesn't have to remind him of things anymore. She continues with her work, writing down formula, while Raymond checks his watch, which is counting down to 0. When it reaches zero, she disappears. Raymond goes to the kitchen and gets breakfast for Kate, who is in a chair staring off into space. He gets her tea and Kate stares at him, saying that she has no idea who he is.
Back at the lab, Peter is trying to figure out the source of the neutron pulses and places it somewhere near the apartment fire and the train incident. Lincoln gets two new reports of spherical time events that relate to incidents four years ago. Walter finally speaks up and explains that the four incidents describe Fibonacci's Golden Spiral and tells them to search in Brookline, Massachusetts.
In Brookline, Raymond tends to Kate and assures her that they will have all the Christmases in the world. He then goes to the basement and enters her calculations, and then powers up an elaborate piece of equipment. When Raymond activates it, time goes back four years, while a timer on the wall displays 47 minutes. He goes back upstairs and finds Kate working on her equations again. She reminds him of the things he has to do while he glances at his watch and the time counting down from 47 minutes.
Peter, Olivia, and Lincoln canvass Brookline and she asks Peter if he has something on his mind. He asks her if any of her dreams involved them being in a park with Walter on a swing, and if she had a feeling that she knew him. Olivia says that Peter is a stranger and that she didn't have any feeling of familiarity.
At home, Raymond notices the agents outside. He tells Kate that there's something she needs to know and takes her to the basement to see his equipment. Raymond explains that he built the time chamber from her work after three years and that it only works for 47 minutes at a time. He needs Kate to complete the equations so they can keep the chamber open permanently, and she asks what year it is. He admits that it's 2011, even though she believes that it's 2007.
An agent approaches Raymond's house and Olivia and the others see him first enter a bubble of distorted time and then disintegrate, screaming. Olivia contacts Walter and then approaches the house. He has her spray fingerprint powder, delineating the spherical field and confirming that it surrounds the entire property. Peter says that they need a mobile Faraday Cage to block out the electromagnetic fields. Walter overhears him on the phone and angrily insists that he knows what a Faraday Cage is, and starts putting it together. Peter and Lincoln go find a map and try and track where the next event will occur based on Walter's spiral.
In the house, Kate watches them and warns Raymond that some things were only meant to be a theory. He insists that they don't have time to discuss it, and Kate asks what happened to her that he created the time chamber. Raymond finally explains that he lost her.
Broyles confirms that Raymond is an electrical engineer and Kate is a theoretical physicist, and that Kate suffered from early-onset Alzheimer. Meanwhile, Peter and Lincoln confirm that the next incident will be at a traffic tunnel that didn't exist four years ago. As Lincoln goes to supervise the evacuation of the tunnel, Astrid arrives with Walter's harness. They realize that Pete will have to go in because he's the only one with the scientific knowledge to shut down the machine. Walter, watching on the remote camera, warns that if the time chamber overrides the Faraday harness, Peter will be killed just like the agent.
Peter approaches the edge of the time field, turns on the Faraday harness, and reaches his arm into the field. Once he's sure it works, he steps through the field while Walter concedes that Peter's idea was a good idea.
In the house, Kate tells warns Raymond that she already solved the equation. She hasn't written it down yet, but she has it. They hear Peter walking around upstairs. When Peter comes downstairs, Raymond knocks him out.
As Olivia tries to reestablish contact with Peter, Lincoln calls to show them the advancing edge of the time field, and the non-existent tunnel on the other side. People are still trapped in the tunnel due to the panic.
In the basement, Peter wakes up as Raymond explains to Kate that he was unable to get the time chamber to work until just a day or two ago, and that he believes they can establish it permanently. Peter grabs a baseball bat and tries to shut it down, but the Greens warn that if it isn't shut down properly it will destroy the entire city block. When Peter explains that there's already been one death, Kate realizes that the time chamber is causing displacements. She offers to shut the machine down in return for immunity for Raymond, explaining that he couldn't have known what would have happened.
As Peter talks to Olivia, Raymond tells Kate that when she got sick, he didn't have the chance to be there for her and that he thought they'd have more time. Kate says that what they have isn't living but Raymond insists there's nothing else he can do for her and that what's waiting for her is horrible. He asks her to write the completed equation in the book and insists that he won't give up. Kate contemplates the idea and Raymond assures her that they can build the time chamber again, somewhere safe. He hands her a pen and she writes down the equation, crying.
In the tunnel, water begins to flood in through the time distortion.
Peter returns to the basement and tells them that he's confirmed that Raymond won't be prosecuted. Kate finishes writing and the couple kisses. She tells Raymond that she loves him and he shuts down the time chamber. The 2007 Kate disappears at the same time as the temporal displacement sphere in the tunnel.
Later, the FBI takes away the equipment while Raymond tries to reassure Kate. He tells her that he'll be back in a few hours and leaves her with a nurse. Raymond then makes sure that no one is looking and takes out the book with the finished equations. However, he discovers that Kate crossed out all of her work and left him a note telling him to repay her by living his life.
At Fringe headquarters, Olivia tells Peter to wait while she talks to Lincoln. Broyles comes over and congratulates him on his work, and notes that apparently Peter didn't cause the distortions. However, Peter says that the only reason Kate's equations worked was because he came back through time. All of the people he knows are gone, and he has to figure out a way to get back to his own timeline. Broyles tells him that he's arranged for him to stay in the faculty home he was staying at with Walter in his own timeline.
Peter and Olivia go to the house. She warns him that there'll be an FBI agent outside his door, but Peter wonders where he could possibly run to. Olivia says that she'll try to convince Walter to help him, and then tells Peter that she's realized that she was important to Peter in his timeline. Peter admits that his Olivia is, and Olivia says that she hopes Peter will get back to her.