At a business mall in Boston, Massachusetts, Neal picks up his coffee and a friend comes over. Neal collects his coffee and heads outside, but then clutches at his stomach and collapses. Fumes emerge from his blackened mouth as he falls over, burning from the inside, and everyone walking in the area collapses as well, suffering from the same symptoms. One woman realizes that they all died when they moved and tells the few surviving people in the area to stand still as well.
Olivia and Peter are in bed discussing where to move in together. She asks if any of the apartments have a nursery and Peter smiles in pleasure. As they start to kiss, they both get phone calls. Walter and Astrid are already at the mall, where the surviving pedestrians are still standing stock still. The technicians inform them that there are no airborne toxins and Walter goes into the area. He spots the phone belonging to the first victim and confirms that he used it to pay for his coffee. When Peter and Olivia arrive, Broyles brings them up to speed
Walter examines one of the corpses and chats with it, while a nearby woman, Jessica Holt, asks if she's going to die. He admits that he has no idea, and explains that he's a scientist and asks to take a blood sample and is impressed when she can make a joke given the situation. As Walter takes the sample, he notices that she has smudges on her fingers and Jessica says that she got it from the escalator railing. They analyze the blood and confirm that there is some kind of viral incursion. Walter wonders where the virus originated since not everyone was on the escalator. A technician finds a device attached beneath the escalator and Walter realizes that it's infested with nanites. He explains to the others that the nanites were overloaded by the biokinetic energy of anyone infected. The longer they're in the bloodstream, the more sensitive they become. Walter says that they have to get the people to the lab for further study.
Astrid talks to Jessica and assures her that her medical costs will be fully covered. She volunteers to let them use her and assures Olivia that she understands the risks. Walter has the EMTs put Jessica on a solid-board stretcher and covers her with ice packs. Once they get her to the Harvard lab, Walter and Astrid go to work. Jessica tells Olivia that she works as an ER nurse and asks her to get her phone for her. She calls her husband, Mike, and tells him that he needs to pick up Sarah after school. She admits that it's not his day and promises to explain it to him later.
Jessica wonders how long until they have an antidote and Olivia checks with Walter. Walter says that they're seeing first results but admits that it will take at least a few more minutes. Jessica's body temperature begins rising and Walter tells Olivia to keep her calm. The woman tells Olivia to stay away from her but Olivia grasps her hand... and the power in the lab goes out as Jessica's temperature drops to normal. After a moment the power comes up and Olivia admits that she has no idea how she saved their patient.
Peter administers the antidote to neutralize the nanites while Olivia asks Walter if he knows what happened to her. He guesses that the cortexiphan treatment gave her control over molecules, allowing her to slow the molecules down. However, Walter has no idea how she managed to trigger the power in this case. Olivia takes Jessica home and thanks her for her help. Jessica thanks Olivia for saving her life, and Olivia notes that not everyone would volunteer. The nurse explains that she did it for her daughter and promises to call if she has any more symptoms. As Jessica leaves, Broyles calls Olivia and tells her that they know who is responsible. Back at Fringe Division, they go over the security footage and confirm that Jones planted the nanite-generating device. They wonder what Jones' plan is given his scheme of collapsing the two universes, and figure that he's come up with another way to accomplish his goals. Peter warns that Jones won't give up.
At the lab, Walter studies the nanites and discovers that they have a chimeric structure. Astrid gets a call from Olivia and tells Walter that Jones is involved, and Walter explains that Jones is working with someone else to create the nanites. He tells Astrid that there is only one person who would construct the particular chimeric pattern.
Jones informs his superior that Olivia has stopped them again. However, William Bell says that he shouldn't be so sure. Jones is surprised at his lack of concern and then notices that Bell has never moved the pieces on the chessboard in his cabin. Bell says that it's been twenty years since the last move and that the master player must know when a piece is most valuable and then sacrifice it. He points out that the most valuable piece is the bishop, and to win the game they must sacrifice the bishop. Jones understands and assures Bell that he'll attend to it promptly.
Walter tells Nina and Olivia that Bell is alive and that the work had to be his. Nina confirms that she saw Bell's body after he died in a car accident on Christmas, seven years ago. However, Walter remembers Bell coming to see him on New Year's Eve, seven days later. Nina finally tells him that Bell had lymphoma and took his own life on his own terms. She doesn't believe that Bell would try to destroy a universe, and Walter says that he'll prove it.
Walter, Olivia, and Peter go to St. Claire's and Walter examines the table in his old room where he wrote his equations. As he leaves the room, an orderly remembers him and asks if he's back to stay. Shaken, Walter stares at him and Peter arrives to escort him to the administrator, Dr. Benlo. She explains that their record keeping system is out of date as Walter goes over the visitor logs from seven years ago. They don't keep the surveillance video for more than two years, and the logs don't show any indication that Bell was there. Olivia suggests that he might have been hallucinating due to the shock treatment, but Walter assures her that his hallucinations were never bipedal. He starts licking the visitor logbook and asks Benlo if he can take them, and she agrees.
That night, Peter and Olivia are making supper and Olivia cuts her finger with a knife while cutting vegetables. She admits that she was distracted thinking about Jessica and how she almost lost her child just by encountering them. Olivia wonders what the odds are that they'll have a normal life and worries about her cortexiphan powers. Peter assures her that they'll figure it out together and kisses her, and tells her that he won't lose her again. The lights outside suddenly brighten and they look out the window.
Broyles is leaving work when he sees a bright flare of sunlight coming from the sky. He stares at it as it smashes straight down through a building, destroying it.
As Peter and Olivia drive into town, they contact Walter, who says that Jones is focusing the power of the sun using some kind of orbital satellite. Astrid gets him a geological file of Beacon Hill confirming that there is a subterranean oil deposit in the area. If the focused sunlight hits it, it will ignite and destroy Boston. Walter tells them to evacuate the entire city, while Astrid identifies two unidentified radio frequencies in use. Walter recognizes the frequencies as Bell's work and starts writing.
Once he's performed his calculations, Walter directs Peter and Olivia to a Chinatown address and tells them that Jones has commandeered two commercial satellites and triangulated the signals to the address. He then makes a lemon cake and explains to Astrid that it's about Bell.
Peter and Olivia arrive at the address and spot two antennae on nearby rooftops. They split up to shut them down, unaware that Jones is watching them from nearby. Jones watches Peter climb up to the rooftop and then goes after him.
Walter cuts open the lemon cake and explains that he laced it with pig brain and page from the log book. He explains that heated cortexiphan stimulates cell regeneration, producing the fingerprints on the paper. However, they are too badly smudged to verify that they belong to Bell. Astrid notices a brown mark and Walter studies it, while the lemon cake regenerates itself. Walter tastes the paper and confirms that it's Chilean almond oil: Bell's favorite food. He then leaves to find Bell at the A1 Import warehouse where he purchased the almond oil. Astrid objects but Walter insists that he has to prove that he's not crazy. He tells Astrid that he can pursue it on his own, but then remembers that he can't drive and comes back for her.
Olivia breaks open one control panel and coordinates with Peter to shut it down at the same precise time. They shut down the beam, but Jones attacks Peter from behind. While they struggle, Olivia draws her gun and tries to get a bead on Jones. Two security men arrive and order Olivia to drop her gun, but when she does they mimic her movements and drop their guns. She then looks across the street, concentrates, and controls Jones into letting Peter go. She then manipulates Peter into hitting Jones, knocking him back into the antenna. Jones realizes that he was the sacrifice all along and disintegrates into dust in a matter of seconds.
At Boston Harbor, Walter directs Astrid to A1 Imports and confirms that the door is unlocked. A man greets them and alter asks to speak with Ms. Lynn Weisberg. The man explains that the company went out of business three years ago. Astrid notices that the man, Tom, has a holstered gun and thanks him for his help. Once he leaves, she tells Walter what she saw. They hear wild animals crying and Walter goes to investigate, and Astrid follows him. They find cargo containers filled with crates, and Tom and his men capture them. Astrid knocks one down, grabs Walter, and runs off between the cargo containers. However, Tom shoots her and she collapses to the ground. Bell comes out of the shadows and says hello to his old friend.