At a business center in Boston, a man named Neal comes down the escalator and collects a cup of coffee. As he goes outside, he starts to burn from within and then collapses. Anyone walking nearby gets the same symptoms and burn up from spontaneous combustion. One woman realizes that only the people who are walking are dead and tells everyone else to freeze.
Peter and Olivia are at home planning where to move and Olivia mentions that they need a home with a nursery. As they kiss, they both get calls summoning them to the business center. Walter and Astrid are already there and confirm that the remaining pedestrians are still standing still. The technicians confirm that there are no airborne toxins and Walter starts examining the vicinity.
Peter and Olivia arrive and Broyles brings them up to speed. One of the surviving pedestrians, Jessica Holt, asks Walter if she’s going to die. He admits that he has no idea and asks to take a blood sample, and Jessica jokes with him as she gives her permission. Walter notices smudges on her fingers and Jessica says that she got them from the escalator railing. He takes a sample of the smudge and analyzes the blood, and Astrid confirms that there is a virus at work. Walter isn’t able to find a common pattern until a technician finds a high-tech box inside of the escalator mechanism. Walter examines it and realizes that it is manufacturing nanites. The nanites bonded with anybody in the vicinity, and were overloaded by the hosts’ biokinetic energy. When people moved, the nanites gave off extreme heat. Walter warns the others that the longer the nanites are in the host bodies, the most sensitive they become.
Once they inform Jessica that they will take care of her, she volunteers to let them move her to the lab where Walter can conduct their experiments. They strap her to a solid-board stretcher, pack her with ice, and move her to the Harvard lab. As Walter, Peter, and Astrid try to create an antidote, Olivia chats with the woman and gets her phone. Jessica then calls her husband Mike, and has him pick up their daughter. She avoids telling him what has happened to her and says that she’ll explains later.
Olivia checks with Walter, who warns that the antidote will still take a few minutes. Jessica’s body temperature begins rising and Walter tells Olivia to help Jessica focus. Olivia takes her hand and tells her to breathe, but Jessica’s temperature continues to rise. Olivia stares at her helplessly... and then Jessica’s temperature drops to normal as the lights flicker. The power comes back up and Olivia admits that she has no idea how she did what she just did.
As they give Jessica the antidote, Olivia asks Walter if he knows what is going on. He suggests that her cortexiphan abilities let her manipulate molecules, slowing down the nanites in Jessica’s body. However, he has no more idea how she did it than Olivia does. Olivia escorts Jessica to the police car that will take her home and thanks her for her help. Jessica thanks Olivia for saving her and explains that she volunteered so that her daughter Sarah wouldn’t grow up without a daughter.
Broyles summons the team to Fringe Division and shows them footage from the business center. Jones is the one who put the device in the escalator and they figure it’s part of his new scheme to destroy the two universes and create his own. However, they have no idea what he intends now that the bridge has been turned off, but figure that he won’t give up.
Back at the lab, Walter analyzes the nanites and recognizes their design. Astrid receives word that Jones is involved, but Walter tells her that Jones is working with someone else, and there is only one person who could construct these particular nanites.
Jones boards a ship and goes to the cabin of the man he works for: William Bell. When Bell gets word that Olivia thwarted their plan, he tells Jones that he shouldn’t be so sure. He indicates a chessboard where he has only made one movie in twenty years, and explains that a grand master must know when a piece is most valuable and when it will make the best sacrifice. He shows Jones the bishop and says that they must sacrifice, and Jones says that he’ll tend to it promptly.
Walter and Olivia go to see Nina and tell her what Walter suspects. She reminds him that she saw Bell’s body after he died in a car accident on Christmas Eve, seven years ago. Walter remembers seeing Bell at St. Claire’s on New Year’s Eve a week later, but Nina assures him that she knows when Bell died. She explains that Bell was dying of lymphoma and engineered his own death in the car so he could deal with life on his own terms. Nina doesn’t believe that Bell would want to destroy a universe, and Walter says that he’ll prove Bell is still alive and responsible for Jones’ activities.
Olivia, Walter, and Peter go to St. Claire to check the records. Walter goes back to his old cell and examines the equations he wrote. When he steps out, an orderly recognizes him and asks if he’s back to stay. Shaken, Walter walks past him and Peter escorts him to the administrator’s office. The current administrator, Dr. Benlo, is helpful but admits that their bookkeeping system is out of date. Walter goes over the visitor logs from when he was incarcerated and finds no mention of Bell, while Peter confirms that the video surveillance is only kept for two years. Olivia wonders if Walter might have hallucinated Bell, but he assures her that he didn’t and starts licking the logbook. After a moment he asks Benlo if he can take it and she agrees.
That night, Peter and Olivia are at home and she cuts herself making supper. She admits that she was distracted by what happened to Jessica and how she almost died after a brief encounter with a Fringe event. Olivia worries that the odds are against her surviving, much less having a normal life given her cortexiphan powers. Peter assures her that they’ll figure things out together. However, they’re interrupted when a blind light shines through the window.
Broyles is leaving work when he sees a beam of concentrated sunlight slam out of the sky and destroy a building, and then start drilling into the earth beneath.
Peter and Olivia drive downtown and Walter calls to tell them that Jones is using two private communication satellites to refocus sunlight and beam it to earth. Astrid checks the geological files and confirms that the site where the beam is striking contains a recently-discovered subterranean oil deposit. When the beam ignites the oil, the entire city of Boston will go up in flames. Astrid confirms that two separate radio frequencies are being used and Walter realizes that Bell is responsible. He triangulates the beams and directs Peter and Oliver to an address in Chinatown where the signals are originating. Walter then makes a small lemon cake, assuring Astrid that it involves Bell.
At the address, Peter and Olivia find the two antennae on two adjoining rooftops. They split up to shut them down, and Jones emerges from a nearby car and goes after Peter.
Walter cuts open the lemon cake and explains that he used it to grow pig brain. He informs Astrid that heated cortexiphan causes cellular regeneration, and that the pig brain has cortexiphan in it. The cortexiphan brings out the old fingerprints on the logbook but they’re too smudged to identify as Bell’s. Astrid points out a brown mark and Walter licks it, confirming that it’s Chilean almond oil. He tells Astrid that it was always Bell’s favorite and that he got it from A1 Import, and sets out to prove that Bell is there. Astrid objects but Walter insists that he’ll do it himself to prove he’s not crazy... and then asks her to drive him since he doesn’t have a license.
Working together, Olivia and Peter open the control panels on both antennae and shut them down simultaneously so that the beam won’t go out of control. However, Jones sneaks up on Peter and attacks him. As the two men struggle, Olivia tries to draw a bead on Jones. Two security guards arrive and order her to drop her gun. She reluctantly does so and is surprised when the two guards mimic her action, dropping their guns. Thinking quickly, Astrid turns toward Peter and Jones and mimics Jones being thrown clear. He throws himself away and Olivia than manipulates Peter into punching Jones, knocking him back into the antennae. The electrical shock sets off a chain reaction in Jones’ metabolism, causing him to start disintegrating. He realizes too late that Bell intended him as the sacrifice, not Peter.
Astrid drives Walter to Boston Harbor and he insists on storming into A1 Import’s warehouse. A man, Tom, is inside, but explains that the company shut down years ago. Astrid notices that he has a hidden pistol and apologizes, thanking him for his help. Once Tom leaves, Astrid tells Walter that they need to get out. However, Walter hears the sound of animals deeper in the warehouse and runs off to investigate. Astrid follows and they find several cargo containers with sealed crates. Before they can investigate further, Tom and his men find them and hold them at gunpoint. Astrid manages to disarm one and runs off into the maze of containers with Walter. However, Tom finds them and shoots Astrid in the chest. As she collapses to the ground, Bell steps out of the shadows and says hello to Walter.