Several weeks ago, David Robert Jones escaped from Wissenschaft Prison in Germany utilizing teleportation. The German authorities sealed the prison but have no idea how Jones escaped.
Two weeks later, Olivia arrives at the lab at Harvard and informs Peter and Walter that Jones escaped. Jones was working with Mitchell Loeb, who stole Walter's invention. Olivia wants a description of it and Peter points out that his father sugarcoated the description last time he explained it. Walter admits it's a teleportation system, and that anyone using it would need to undergo weeks of depressurization.
In a secret facility, Mitchell Loeb's men finish depressurizing Jones and remove him from the barometric chamber. He thanks them for his efforts and checks to determine the equipment he asked for has been assembled. As he takes a sip of tea, his hand starts to shake.
In Boston, a man wearing rubber gloves pays for a newspaper with a $2 bill. He leaves without comments as the newsstand owner, Thomas Avery, takes the bill. Another customer comes by and chats with Tommie Avery, who thinks he has something in his eyes. In a matter of seconds, skin grows over his eyes, mouth, and nose and he falls to the sidewalk, suffocating.
Charlie is tracking down financial records on Jones' lawyer, Salman Kohl. He kept a slush fund under an assumed name and Charlie figures it's something less ordinary than a mistress.
Olivia meets with prisoner Mitchell Loeb and reveals that she knows he helped Jones escaped. Loeb isn't interested in working with her until she points out he's being transferred to a maximum-security prison. Loeb says it doesn't matter, that Jones is just one member of an army, "what is written will come to pass," and that nothing she can do will stop them. Broyles calls and tells her to collect the Bishops and meet him at Boston General Hospital.
Walter examines Tommie's corpse and realizes that ceramides are responsible. Olivia believes that Jones is responsible but Broyles wonders why they would be targeting a newsstand vendor. Olivia checked with a German contact and determined that Jones' ZFT organization, the letters stand for "Zerstorung durch Fortschritte der Technologie." It translates as "Destruction by Advanced Technology," a self-published anonymous manuscript. The manuscript was destroyed ten years ago and Olivia hopes that Peter can use one of his "weird connections" to trace the manuscript.
Walter takes Avery's corpse to the Harvard lab and extracts gas from his lungs. Meanwhile, one of Charlie's underlings has obtained a list of U.S. businesses that Jones' lawyer incorporated.
Peter takes Olivia and meets with a book seller, Markam. He asks for a copy of the ZFT manuscript and Markam says he'll do what he can.
Charlie reports to Broyles on a building in Austin that was abandoned until two weeks ago when the power was turned back on. Broyles starts to call for a warrant but an assistant informs him that Jones is downstairs in the lobby. Agents surround Jones, who says he will speak only with Dunham. They place Jones in an interrogation room and find an unmarked key on him. They figure that Jones wanted them to find the key. Jared Harris doesn't want to negotiate or let Dunham talk to Jones. She figures that Jones is responsible but Harris tells her to go on the raid in Austin and find evidence to connect Jones to Avery's death.
Markam finds a copy of the ZFT and Peter calls Olivia to inform her that it talks of technology destroying the world. Further, it warns that the apocalypse is coming and it will come as warfare. Dunham and the others enter the building and find discarded food and equipment, including a barometric chamber, but no inhabitants. There's also a sketch of Olivia in Jones' hand.
Harris talks to Jones, who still refuses to talk to anyone but Olivia. He asks for several pieces of equipment, including Harris' analog wristwatch.
As the agents search the building, one of them finds a $2 bill in a drawer. Olivia and Charlie are downstairs when they hear the agent scream. They run upstairs to discover that his orifices are sealing over. They try to perform a trachectomy but the hole seals over and the man dies.
Olivia and Charlie return to headquarters to discover that Harris is assembling the components that Jones requested. Olivia takes them into the interrogation room and demand answers. Jones takes the components and builds a scrambling device to prevent anyone outside the room from listening in. Jones, who is clearly suffering from some illness, explains that Avery was used as an example and a warning. He wants Olivia to pass a test and tells her to take the key to an amusement park. When he gets worse, Jones explains that when he was teleported, he suffered from side effects and the task he has for her may help to cure him. Jones explains that his colleagues are using a white van transporting a bomb that will kill several hundred people the same way as Avery and the agent. Harris comes in to order Olivia out, and Jones assures her that if he wanted to harm her, he could have done so a long time ago. Olivia tells them to track down white vans while she gets a massage.
En route, Olivia calls Peter, who confirms that the victims were dosed by a powdered toxin absorbed through the skin. Walter is working on an antidote but doesn't have anything yet. Peter is still translating the ZFT manuscript and promises to get back to her when he has more information. Peter hangs up and discovers that Walter has been reading the manuscript. He insists on reading a passage which speaks of other universes and the way to travel between them has been discovered by other beings with advanced technology. Their arrival will be heralded by a series of unusual events and ultimately only one world will survive.
Olivia goes to the amusement park and uses the key to acquire the various items that Jones has left for her. A letter explains that she should take the first test only. The first test involves a series of small light bulbs that Olivia has to turn off using the power of her mind. Walter notes that the instructions refer to unwilling "recruits" that will eventually become soldiers. Olivia tries to shut off the lights without success. Charlie calls to inform her that they trace the white van but it was rented to an Olivia Dunham: Jones is playing with them.
Olivia goes to see Jones again and Harris objects. She warns him that they have less than seven hours and Jones wants her. Harris agrees and Olivia talks to Jones. She reveals that she's read the manuscript and he explains that she was treated with cortexiphan. They kidnapped her to test her with a spinal tap and confirm the treatment. Olivia has never heard of the drug or received any such treatment. He insists she can pass the test and says she has to cooperate. Jones collapses and Olivia has him taken to the lab. Walter determines that Jones is suffering from cellular collapse and tries to stabilize him. Peter talks to Olivia, who has learned that cortexiphan was a drug patent to Massive Dynamic but never approved by the FDA. Olivia suggests that Peter open up the light box and come up with a way to fake the test.
Olivia meets with Nina Sharp and asks about cortexiphan. As she runs a check, Olivia notices that Nina's prosthetic arm is acting up. Nina explains that Dr. Bell developed the drug in 1981, and that it was intended to prevent the limitation of the potential of the human mind. The drug was administered to children but there was no success and Bell abandoned the research two years later. The trials took place at Ohio State University, and she was in Jacksonville, FL in those two years, with her father at a military base.
Peter reprograms the light box and they revive Jones so he can witness Olivia "pass" the test. Once she does, Jones gives her the address and floor where the device is located. Olivia, Peter, and Charlie arrive there only to discover the device is rigged with the same lighting system as the first test. The bomb squad can't move or defuse it and its attached to a window to blow outward. Olivia calls the lab and talks to Jones, who assures her she can do it. She says that if he doesn't tell her how to disarm it, she'll die, but Jones assures her that he has faith in her.
Olivia has no choice but to try and shut down the lights. With a minute left, Peter starts to leave but reconsiders. He watches as Olivia concentrates on the lights and one by one they go out. With two seconds left, the last light goes out and Olivia admits she has no idea what she did. At the lab, Astrid tells Jones that Olivia succeeded.
Olivia figures that the lights were some kind of trick but Peter assures her that what she did was amazing. She figures that the whole was a setup for Jones to meet Walter. Peter offers to buy her a drink but she plans to go to Boston General where Jones has been taken.
At the lab, Astrid admits to Walter that the teleportation device is cool despite the fact that it kills you. Walter notes that it does something unthinkable, but it doesn't kill the teleportee.
Olivia arrives at the hospital and discovers that someone or something smashed a hole in the wall of Jones' room and abducted him. Two words are written on the wall: "You passed."
Walter goes over the typewritten ZFT manuscript and notices that the "y"s are out of alignment.
Olivia is at home when Nina calls to tell her that her hand is back to normal. Nina tells her that she checked and cortexiphan was also used in trials in Jacksonville, FL at a military base.
Walter opens a cabinet in his lab and takes out an old manual typewriter. He starts typing and realizes that the "y" key is out of alignment.