FBI Office. Broyles briefs a room full of FBI agents on ZFT, a terrorist organization whose modus operandi is to use advanced technology for destructive purposes. The group's name is taken from the German translation of a manifesto entitled, "Destruction through Advancement of Technology." Recent evidence indicates that ZFT might be funded by William Bell, founder and chairman of Massive Dynamic.
Downtown Boston. A troubled woman, SUSAN PRATT, rides a bus. She seems to be in respiratory distress. As the rests her head against the window, condensation appears on the glass. A newspaper nearby begins to singe and curl. Panicking, she forces the bus to stop and gets off. Standing on the sidewalk, the woman suddenly goes up in flame -- and then explodes in a fiery ball.
The Harvard lab. Walter is paging through his copy of the ZFT manifesto. He tells Peter he needs to show him something. He takes out an old typewriter and types out a single word: "Mystery." Both the letters 'y' are oddly raised above the other letters -- a peculiarity matched by the manifesto's text. Walter remembers the day when Belly -- William Bell, his old lab partner -- bought this typewriter. William Bell wrote the manifesto!
But Walter insists that William Bell is not a bad person, and he couldn't be behind the terrible activities of ZFT. The manifesto includes numerous references to a "Chapter of Ethics" that is now missing. Someone must have removed the chapter to suit their own purposes, and Walter intends to prove it.
The team arrives at the scene of the human explosion. Walter says they may be dealing with a case of spontaneous human combustion, but he'll need to do an autopsy. Olivia, looking at the two charred bodies, says she'll have them transported to the lab. Wait, bodies? Walter asks if there was another. Olivia looks back down and sees that now there is only one. Olivia is clearly confused, but she says nothing.
Nina Sharp arrives at Broyles's office, having caught wind of the FBI's investigation into Massive Dynamic and William Bell. Broyles says they have evidence of Bell's involvement in biological attacks. Nina insists that William Bell is not a terrorist, and not the enemy. Broyles would like to hear that from the man himself, but Nina says Bell is traveling abroad and conveniently unavailable.
At the lab, Walter explains that the human body contains a massive amount of potential energy. But Peter says it's one thing to have the energy, quite another to release it. Walter hypothesizes that the spark may have been provided by a subatomic particle, the pyroton, whose existence has not yet been proven. In order to prove his theory, he needs to use the electron microscope in the lab, but Peter has disassembled it for some project he's been working on. This greatly annoys Walter.
Olivia meets Broyles in his office, which has apparently been rearranged. But when she mentions the new arrangement, Broyles is confused. Broyles shows her a crime scene photo of the two victims in the explosion. Wait, wasn't there only one victim? Then Broyles, dressed differently, enters the room and asks if Olivia has any new info on the explosion victim. Olivia is unsure what is going on, but before she can fully react --
Sanford Harris arrives to demand an explanation for the ongoing investigation of William Bell and Massive Dynamic. He tells them to drop the case, but after he leaves the room, Broyles gives Olivia permission to continue the investigation.
In the lab, Walter and Astrid are examining the charred body. Astrid scans Pratt's jawbone, looking for a dental record match. Walter needs his Geiger counter, but it turns out Peter cannibalized that, too. Astrid gets a dental record match: Susan Pratt.
Olivia and Charlie investigate Susan Pratt's apartment. It's a Spartan place, with few personal effects. Her closet is filled with gray and black clothes. Olivia finds a $30,000 check from someone named Isaac Winters. Charlie discovers that the bathroom is a charred ruin, as though an explosion of some kind took place there.
At the lab, Walter wants Frankenberry cereal because that's what he was eating back when he shared the lab with William Bell, and eating that cereal might jog his memory about the manifesto's lost chapter. But the store didn't have Frankenberry, so Peter bought him Berry Boom instead. Olivia says there were other fires at Susan Pratt's apartment, which leads Walter to rule out spontaneous human combustion (which is, by its nature, a one-time event). His new hypothesis is pyrokinesis, the ability to create heat with the mind. It is a form of telekinesis that excites objects at a molecular level, causing heat to generate and releasing then releasing the energy. But without training on how to direct the heat outside of her body, Susan Pratt must have accidentally blown herself up. Olivia wonders whether she was born with this ability, or someone else did it to her.
Charlie and Olivia visit the office of Isaac Winters. Olivia uses a lock pick to open the door. Inside, they play the messages on his answering machine. The first is from Susan Pratt, who says Winters told her to call if anything strange started happening. The second call is Susan Pratt again, scared this time, wondering what is happening to her. Olivia walks out of the building, sees an ambulance going by, and then notices the entire Boston skyline is on fire! But when Charlie interrupts her, she turns back to see the skyline is back to normal.
Back at the lab, Olivia has finally told the group what is happening to her. Walter says hallucinations have many different sources: sleep deprivation, concussion, brain tumors... Olivia says she feels like she's losing her mind. Walter suggests another possibility: she is experiencing a form of extended d?j? vu, which is somehow related to the pliability of space-time. Walter explains that while we experience time as a linear progression, in fact every choice we make creates parallel universes. As a result, time is more like a branching tree of alternative realities. D?j? vu, he says, is just a brief glimpse of an alternative reality. You feel like you've been somewhere before because you actually have been there in another reality. But Olivia wants to know why she is experiencing these extended episodes of D?j? vu. Could it be a result of the Cortexiphan drug she was dosed with as a child?
Astrid arrives with the photo of another victim like Susan Pratt, which she found on the conspiracy website of Emmanuel Grayson. Peter and Olivia visit Grayson in his apartment. Peter asks where the explosion shown in the photo occurred. Grayson says it happened in Budapest. Hungarian police say the victim was attacked, but that's not true. In fact, Grayson says, the victim was the result of unethical experiments carried out by none other than William Bell. Bell is trying to activate the subjects of his experiments; some can handle it, others can't. But why? Grayson says its part of a plan to create super soldiers to defend us in the coming war, just like Khan Nunien Singh. Yes, that would be Khan, as in "The Wrath of...," a villain in the Star Trek universe. And this coming war will be against the Romulans. And then Grayson reveals that he is actually Spock. Clearly, the man is a nutcase.
Nina's conversation with a prime minister is interrupted by another call. Clearly alarmed, she tells her caller to do nothing until she arrives. Then she tells her chauffer to take her to her helicopter.
Olivia speculates that Grayson, though crazy, might be right. Not about being Spock, but about Bell's drug trials. Olivia thinks she might be able to use her visions to solve the case. Maybe she can visit a parallel reality to help understand what's happening in this reality.
Harris gives Olivia a summons for a psychiatric evaluation. She confronts him. Harris says Olivia's analysis borders on the paranoid, and her recent behavior has been erratic. Olivia says she's done everything in her power to work with Harris, but now she's done. She will not let him obstruct her investigations any longer.
As Olivia goes to pick up the telephone, she looks around the room and sees that everything is slightly different. The agents seem tired and harried. Charlie gives a shoot to kill order to other agents before turning to Olivia. There's a scar on his face that wasn't there before. Olivia asks about the Pratt case. Charlie has nothing new and seems uninterested. They have half of Boston in a quarantine lockdown, and she's worried about a pair of twins? Olivia sees, once again, the photo of two charred corpses. And then, abruptly, the office returns to normal.
Now Olivia suspects Susan Pratt had a twin. An FBI tech finds an additional facial recognition match on Pratt's features: NANCY LEWIS, a woman whose identical twin who went missing eleven years ago. The missing twin might have be Susan Pratt. Fortunately, Lewis is a Boston area local.
Nancy Lewis's apartment. Nancy opens her front door... and is greeted by Isaac Winters.
Peter and Olivia arrive at Nancy Lewis's apartment, but she's gone. The front door is unlocked, so they go in. Inside they find signs of a struggle. Peter notices that the window is partially melted. Could Nancy Lewis be starting fires like her sister? Peter has an idea.
Later. Peter cuts a circle of glass from the partially melted window. Meanwhile, Astrid has brought Peter's device -- the one he's been cannibalizing Walter's equipment to build. Peter positions the glass beneath the contraption's electron microscope portion. Then he explains that he was making this device to digitize Walter's old water-damaged vinyl records. His plan was to use the electron microscope to take a high-res image of the grooves in a record, which the computer would then translate into sound. He thinks the same principle will allow them to read the glass. Nancy Lewis was emitting heat just like her sister, and the heat from her body liquefied the glass slightly, so that sound waves would leave impressions in the glass just like the grooves on a record.
The process begins. At first they get only feedback, and the glass disk breaks. But now they've got the scan of the glass. Peter uses a computer and mixing board to calibrate the sounds, and finally they hear a sequence of noises: Nancy Lewis telling someone to leave... a struggle... furniture breaking... a faint beeping... a man saying "I have her, see you there." Olivia asks Peter to play the "recording" back from just before the intruder started to speak. As he does so, they hear the sound of a telephone dialing. Olivia captures the touch-tones on her phone and dials them automatically. The voice at the other end... is Sanford Harris.
Harris leaves the FBI office. Olivia has been waiting outside, and she tails him. She follows him to a warehouse.
Inside, Harris meet with Isaac Winters. They've strapped Nancy to a chair. Harris says their boss is losing patience, they need Nancy to active now.
Olivia finds an office with pictures of many people tacked to the wall, including Nancy Lewis, Susan Pratt, Nick Lane ("Bad Dreams"), and herself -- apparently all Cortexiphan test subjects.
A shot rings out, and Olivia sees that an agent is down. The shooter is Isaac Winters, who takes a shot at Olivia. Olivia returns fire and hits him. Then she enters the room where Nancy is strapped down -- then Harris shuts the door behind her. Now Olivia is trapped inside with Nancy, who seems to be losing control of her powers. She's about to blow!
Through the intercom, Harris says Olivia must be aggravating Nancy even more than she aggravates him. Either Nancy learns to control her power, or she kills both herself and Olivia. Either way, Harris wins. Olivia explains to Nancy both of them were experimented upon as children. Harris says Nancy lacks the mental strength to control her ability. But Olivia says no, she does have the strength. Olivia tells Nancy to focus on something, anything. Nancy focuses on Harris... and seconds later, he lights up and explodes.
Peter and Walter are eating at a diner. An agitated Olivia arrives while Peter's in the bathroom and confronts Walter. She demands to know what he and William Bell did to her. Susan Pratt, Nancy Lewis, Nick Lane, and Olivia all grew up in Jacksonville. All of them were subjects in the Cortexiphan trials. Walter says those were Belly's trials, not his. But Olivia says he knew what was happening. Walter says he was only trying to help and meant no harm. Olivia insists that he tell her the purpose of the experiments. Walter says they were trying to make the children capable, to prepare them for something terrible coming. But what? Walter doesn't know. What did they do to the children? Walter doesn't know that, either. At last, Walter breaks down, saying he can't remember what they did. Olivia leaves, and Peter returns to find Walter in tears.
In the lab, Walter listens to an old vinyl record as he looks through his record collection... and then he discovers the missing chapter of the ZFT manuscript amongst the albums. He calls out to Astrid, saying he was right! He reads from the Chapter of Ethics: "Our children are our greatest resource. We must nurture them and protect them. We must prepare them, so they can one day protect us." Then Walter turns to see it's not Astrid behind him... it's the Observer. The Observer says it's time to go. Walter puts down the chapter, and goes to get his coat.
Nina Sharp arrives at her condominium and takes the elevator to the penthouse. The elevator doors open to reveal a dark figure, who points a gun at her... and fires.