Broyles briefs his agents on ZFT and their supposed connection to William Bell, who is financing their operation. Their orders are to get actionable evidence connecting Bell to ZFT. Meanwhile, in New York City a young woman, Susan Pratt, runs out of her apartment and tries to hail a taxi to get to the hospital. When she can't, she gets on a bus but notices that the windows are melting and a nearby paper is charring. She quickly gets off and staggers into the street… and then bursts into flames.
Walter is going over the "y"s in the ZFT manifesto and finally shows Peter and Astrid the typewriter in the lab that has the same offset "y". However, although Walter explains the typewriter belonged to William Bell, he doesn't believe that Bell would have typed such a thing and he was no madman. Walter notes that there is a chapter on ethics missing, and believes someone removed the papers to alter the manifesto for their own purposes. Walter says they need to find the original manifesto, which will absolve Bell.
Olivia calls Walter and Peter to New York City where they check on the body. Walter suggests spontaneous combustion. Olivia makes preparations to take the two bodies away… but she's the only one who sees two bodies. As she concentrates, the second body disappears.
Nina comes to see Broyles, having learned about the investigation. She insists that Bell is a hero and has no involvement with ZFT, but admits that Bell is out of the country and not available.
Walter and Astrid begin an autopsy on Susan's body. Peter comes in and Walter asks for his electron microscope, but Peter notes that he's borrowed some of the parts.
Olivia comes to give Broyles her report and notes that he's rearranged his office. As she prepares to canvass the area, Broyles mentions a second victim. A confused Olivia notes there was only one victim but Broyles shows her a photo of two victims: the same two bodies Olivia saw earlier on the street. The door opens and Olivia turns to see Broyles enter the office: the first Broyles disappears and the office rearranges itself to normal. She gives her report but they're interrupted when Sanford Harris barges in and demands to know what they have on Bell. He dismisses their evidence and notes that Bell is connected to the Defense Department. He tells them to drop the case and leaves. Broyles tells Olivia to go ahead with the investigation.
Astrid prepares to do a dental identification on Susan's teeth while Walter realizes the original copy of the manifesto is probably in his files. He looks for a Geiger counter and discovers that Peter has cannibalized it for his project. Astrid identifies Susan's corpse and Olivia and Charlie go to her apartment. They discover that she lived alone, had no friends, and dressed in grey and black. Olivia finds a check from an Isaac Winters, and they discover the bathroom has been severely charred.
Peter and Olivia return to the lab and Olivia tells Walter what they discovered. He realizes that it was pyrokinesis rather than spontaneous combustion, and that some individuals can vibrate the moles of an object, setting it on fire. Walter speculates that it was a newly-acquired ability set off by anxiety and she turned the energy inward rather than release it and kill someone else. What he doesn't know is whether it's a natural ability or the result of some experiment.
Charlie tracks down Winters, a lawyer in Charlestown, MA. Olivia and Charlie go there and discover his office is abandoned. They find an answering machine with a message from Susan begging for help. As Olivia goes outside, she sees fire engines driving by and skyscrapers burning in the distance. Charlie comes out and the seeming vision disappears.
At the lab, Walter checks Olivia but can't account for her seeming hallucinations. He speculates that she's having visions from a parallel reality. However, Walter doesn't know why she's having the visions. Olivia asks if the drug trials she underwent as a child would be responsible. Walter doesn't know, but believes that they mean something to her.
Astrid finds a web site documenting a similar, which belongs to an Emmanuel Grayson. Peter and Olivia go to see him and he suspects Olivia as a FBI agent. Peter manages to convince him to reveal what he knows. The dead man was an American student in Budapest, and Grayson claims that Bell was responsible. According to Grayson, Bell is conducting secret drug trials and the dead man was one of the subjects. Bell is activating his subjects to see which ones can handle the process, and the subjects that survive will serve as super-soldiers. However, Grayson starts rambling about time-traveling Romulans and claims he's Spock. Peter wishes him well and leaves.
Nina is on her cell phone dealing with business when she gets an urgent call.
Peter and Olivia are going over the case at FBI headquarters when Sanford comes in and gives her a new assignment: to report in for a psych evaluation. Olivia angrily confronts him but Sanford refuses to back down and tells her she has no choice. As Olivia goes back to Peter, reality shifts again and she finds herself in the alternate universe. She talks to Charlie, who has a scar near his left eye, and asks about Susan Pratt. Charlie notes that she is one of a pair of charred twins and gives her the file. Olivia then finds herself back in her reality. She runs a check on Susan's twin sister, Nancy Lewis, and locate her address.
Nancy answers the door to find a man, Isaac Winters, there to see her.
Olivia and Peter go to Nancy's apartment and find signs of a struggle. The kitchen window is partially melted and no one is there. Olivia calls a team in and Peter carefully extracts the melted section of window glass. Walter and Astrid arrive with Peter's new project, and Peter explains that it reconstructs audio so he could digitize some of Walter's old vinyl records. He plans to digitize the impressions on the glass and recover whatever was said when Nancy panicked and melted the window. They hear the struggle and hear Winters dial his superior. Olivia uses her cell phone app to dial the recorded number and gets Sanford Harris' phone.
When Sanford leaves FBI headquarters, Olivia and Charlie follow him to a warehouse. They call in a team and break in, while Sanford meets with Winters. They're conducting experiments to "activate" Nancy Lewis. Olivia searches the offices and finds a room with photos of herself and all the other children who were part of the drug trials. One of her agents is show and Olivia disposes of the guard responsible. She spots Winters and is forced to shoot him. She finds Nancy in the lab and goes in to rescue her. Sanford seals her in the containment lab as Nancy starts to panic. Sanford calls his boss and tells him that the project is a success, while Olivia tries to calm down Nancy and help her get control. She tells Nancy to focus and the woman sees Sanford. He begins to sweat and then explodes into flames.
Later, Peter and Walter go to a diner. Peter goes to the restroom and Olivia confronts Walter alone. She demands to know what Walter knows about what he and Bell did to her and the other children. He insists they were preparing the children and something terrible was coming, but he can't remember what. He breaks into tears and Olivia walks away. Peter returns, sees that his father is upset, and takes his hand to comfort him.
Nina comes to see Broyles and warns him that they have an increasing number of Observer spottings. She reminds him of what happened the last time he was seen so frequently and says they need to talk.
Walter is in his lab listening to a record. He finds the original manifesto among his box of records and reads the section about ethics. Someone enters the lab and Walter turns to see it's the Observer. The Observer tells him it's time to go and Walter quietly goes with him.
Nina returns to her apartment only to discover armed men in masks waiting for her.