Wissenschaft Prison, Germany. DAVID ROBERT JONES waits patiently in his cell, drawing the face of a woman on a sheet of paper. His lawyer SIMON COLE enters with his appeal and the items Jones requested. While the lawyer rifles through his briefcase, Jones sneaks up behind him and breaks his neck. He removes Cole's suit and puts it on, swallows some pills, applies eye drops, and puts sunscreen on his face. He stands patiently in the corner as a bright light illuminates him from above. The light intensifies and envelops him...
Little Hill Field, Massachusetts. Out of nowhere, a beam of light appears in the middle of the field, and out of the beam steps Jones.
Back at the prison, German guards rush to Jones's cell to discover the lawyer dead and the prisoner missing.
The Harvard lab. Olivia arrives to find Walter making a mold of Gene's udders. Olivia breaks the news to Peter that Jones escaped. Walter remembers that Jones was working with AGENT MITCHEL LOEB, the man who stole a contraption he had made years earlier and hidden in safe deposit boxes across the East Coast ("Safe"). Olivia asks Walter what exactly that contraption was. Walter says that he created a teleportation system. But if someone were to it, they would require weeks in a decompression tank to survive, and even then would suffer adverse side effects.
Warehouse in an undisclosed location. A small group of men stand around a massive tank as its door is opened, releasing gas and pressure. Out steps Jones. He briefs his team, thanking them for all of their sacrifices. Although calm and collected, Jones is visibly shaking.
A Boston newsstand. A man with latex gloves picks up a paper and drops a $2 bill. The clerk, THOMAS AVERY, puts the bill in the register as he chats with another customer. His eyes begin to form a gooey mucus -- and then slowly begin to cover with skin. The man panics as his eyes, nostrils, and mouth seal over and suffocate him.
At the FBI office, Charlie tells Broyles he's found financial records for Simon Cole, Jones's attorney. Apparently he kept a slush fund under an assumed name to use on his clients' behalf.
Military installation. Armed guards bring out a shackled Mitchell Loeb (last seen in "Bound") to meet with Olivia. She says she knows he and Jones were working together and that he must know Jones's whereabouts. But Loeb won't cooperate in spite of Olivia's threat to transfer Loeb to more dangerous prison. Instead, he tells her it doesn't matter whether she finds Jones, because he's just a part of the army; that "what was written will come to pass" and nothing Olivia does can change that. Then Olivia receives a phone call summoning her to the hospital.
Boston General Hospital. Broyles briefs the Olivia and Peter on the case of the skinned-over newsman, while Walter examines the body. He concludes that the lipids responsible for skin growth have somehow mutated and sealed off all bodily orifices. Olivia suspects this is Jones's work.
Olivia pulls Peter aside and relays what Loeb told her about "what was written." She has a hunch: maybe "ZFT," which they had thought was the name of Jones's terrorist organization, might actually be the name of their bible. Olivia's already contacted the German authorities to investigate this possibility, and they found references to a document by the name "Zerstorung durch Fortschritte der Technologie," which loosely translates to "destruction by advancement of technology." The document, a rare self-published manuscript, was recovered from a crime scene and inventoried, but was destroyed ten years ago. Olivia wonders if Peter might have any "weird connections" that could get their hands on another copy. Peter believes he does.
At the lab, Astrid and Walter perform some tests on the orifice-less body to recover any available evidence. They cut open the man's mouth and capture the putrid gas in an IV bag.
A used bookstore. Peter visits MARKHAM, the shop's crusty proprietor. Peter tells him about the ZFT manuscript and asks if he can find it for him ASAP. If anyone can find this document, it's Markham.
At the FBI office, Charlie believes he may have found something. Jones's attorney leased a warehouse in Allston whose power had been cut until two weeks back, when it was turned on again. As Broyles makes a call to have the place raided, an agent comes in and interrupts. She tells him David Robert Jones is in the lobby. Broyles races downstairs and confronts Jones. Jones calmly announces that he'll only speak to agent Olivia Dunham.
Harris, Broyles, and Olivia watch Jones sitting in the interrogation room from the observation room. Broyles reveals that when they searched his person they found only a key. Olivia wants to speak with Jones, but Harris says that Jones doesn't get to dictate the terms of his captivity. Olivia points out that since Jones has been in town one man has died in a gruesome fashion, and that Jones likely has more terror planned. But Harris refuses to let Dunham interrogate Jones until she gets hard evidence connecting Jones to event at the newsstand.
En route to the warehouse leased by Jones's attorney, Olivia gets a call from Peter. Markham found a copy of the ZFT manuscript in someone's collection of scientific ephemera. He reads an excerpt, which states, "The advances of science ... will, if not carefully controlled, destroy the world as we know it." The book goes on to assert that this apocalypse will take the form of warfare.
As the FBI unit sweeps the warehouse, Olivia finds a drawing of herself on a desk. She knows immediately this is Jones' work. Charlie orders the team to bag and tag everything.
At the FBI, Harris has a go at interrogating Jones, who alludes to the fact that he killed the newsstand man. Then Jones brazenly says that he'll require a few items when agent Dunham comes to visit him: a standard walkie-talkie, a ballpoint pen, an eyeglass repair kit, and an analog watch like the one Harris is wearing.
Back at the warehouse, a young agent finds a $2 bill in a desk drawer upstairs. Olivia and Charlie, downstairs, hear the young agent's screams. They arrive to find the agent's mouth, nose, and eyes covering with skin. He's suffocating to death. Olivia performs an emergency tracheotomy. The agent appears to have been saved... until the skin grows over the hole in the trach tube and the agent dies.
Olivia and Charlie arrive back at FBI headquarters as Harris drops his watch into a paper bag: the items Jones requested. Olivia interrogates Jones, who coughs sporadically, clearly not well. He removes the items from the bag and takes apart the walkie-talkie and Harris's watch. Using all the components, he quickly fashions a bizarre device. Once it's complete, he switches it on and sends squealing feedback into the surveillance room.
Jones tells Olivia that they're now alone; he's jamming the surveillance feed. He tells Olivia that he's planning a far bigger attack using the same method that killed the field agent and the newsman. But before he gives any details, he needs for Olivia to pass a test. He needs for Olivia to take the key that was confiscated from him to an amusement park in Salem, where she will find a package he left for her.
Jones then shudders in pain, and Olivia suggests he needs medical attention. He explains that there's no medical specialist who could help him; being deconstructed and reassembled at a molecular level (by the teleportation device) seems to have certain "unadvertised side-effects." Olivia demands to know about the attack. Jones explains that a device capable of killing hundreds is being transported somewhere in a white cargo van and will detonate in 16 hours. Olivia, thinking she has some leverage, tells Jones that she won't complete the test until he defuses the bomb. Jones says no, she will defuse the bomb.
On her way out, Olivia tells Broyles and Harris she needs them to track down every white cargo van rented in the last 48 hours. Meanwhile, she needs two hours alone.
On her way to Salem, Olivia checks in with Peter. He explains that the toxin used to kill the two victims so far triggers hyperactivity in the protein responsible for scar tissue. Olivia asks if Peter's found anything interesting in the manifesto. He says, "It reads like a happy combo between an anti-science manifesto and a call to arms."
As Olivia arrives at the amusement park and retrieves the package, Walter reads an excerpt from the manifesto in voice-over. According to the manifesto, our universe is only one of many, and that it is possible to travel from one to another. The means of such travel has already been discovered by beings much likely, but whose history is slightly ahead of our own. The repercussions of such travel will manifest themselves as a series of unnatural occurrences, starting small and growing in severity until, ultimately, only one world will survive.
In the lab, Astrid and Peter unpack the box Olivia retrieved from the park. The letter says that the box contains a number of tests to evaluate inherent skills present in certain individuals. Olivia must complete test number one, then go to see Jones so no one else will die. The instructions for test #1 say the "recruit" must sit in front of a wooden box that houses an array of lights. The recruit must focus on the light-board and turn off all of the lights without touching them. In short, Olivia must turn the lights off with her mind. Walter points out that the term "recruit" appears in the manifesto, as a reference to future soldiers in the coming battle. Olivia, despite her skepticism, focuses intently on the lights -- but her ringing phone breaks her concentration.
On the phone, Charlie tells her someone rented a white van in Olivia's name in New Haven, Connecticut. Olivia, now believing this is just a mind game Jones is playing, goes to pay him a visit.
Olivia talks with Jones and admits she didn't complete the test. Jones says it's normal for her to be skeptical, but she was one of a small group of people few treated with a drug called Cortexiphan. That's why they kidnapped her ("Safe" and "Bound"): confirmation of Cortexiphan dosing requires a spinal tap. Olivia's refuses to play Jones's game anymore, but Jones insists that Olivia must cooperate -- and suddenly passes out.
Jones is rushed to the lab, where Walter rushes to stabilize him. Olivia is just getting off the phone with Charlie, who's informed her that Cortexiphan is a drug patented by Massive Dynamic. Olivia tells Peter that Jones is still expecting her to pass the test and she wants Peter to rig it. Peter agrees.
Massive Dynamic. Olivia meets with Nina Sharp, COO of Massive Dynamic, and asks her about Cortexiphan. Nina says that the drug's clinical trials were performed by Massive Dynamic founder William Bell, in order to test his theory that the young brain is infinitely capable of absorbing information at birth but becomes increasingly limited with age. Cortexiphan was administered to young children in the hope that it would limit this degradation. But the drug was only administered in one trial in Ohio in 1981.
In the car, Olivia calls Peter and tells him that she couldn't have possibly been dosed with Cortexiphan, because in 1981 she was three years old and living in Jacksonville, Florida. Peter informs her that he's successfully rigged the light-box.
The Harvard lab. Walter uses an injection to wake up Jones, who thanks Walter for the incredible work that allowed him to escape his imprisonment. Walter tells Jones that he locked away the teleporter for a reason, one which Jones is now experiencing. With only two hours before Jones's device goes off, Olivia performs the light-box test in front of Jones. Peter's rig job works like a charm, so Olivia appears to pass the test. A pleased Jones gives her an address of a building and says the device is on the 47th floor. Olivia calls in an evacuation.
Olivia arrives on the scene, where Charlie tells her the bomb squad can't diffuse the bomb because they've never seen anything like it. When the sees the bomb, secured to a window overlooking the city, she realizes the front panel of the bomb is a light-box identical to the one in the test.
Peter realizes that when the bomb blows, the toxin will spread for miles. Charlie goes to alert the weather service and FEMA. Olivia calls the lab and pleads with Jones to tell her how to disarm the bomb. She can't turn the lights off with her mind, and if she stays to try she's going to die. Jones knew she faked the test earlier, but now she has to pass it for real. Olivia orders everyone out. Peter tries to talk her out of it, but she ignores him. Peter runs for the exit. Meanwhile, Olivia focuses on the light-box. Peter reluctantly returns to watch. All sound disappears, her focus becomes complete... and gradually, one by one, all the lights go out.
Afterward, Olivia insists she didn't do anything. Jones planned the lights to turn out just in time; it was just a mind game. Peter, for a change, is not the skeptic. He saw that Olivia was in the zone, and something amazing happened.
Back at the lab, Astrid admits to Walter that she's pretty impressed by his teleportation device, even if using it does kill you. Walter says the device does something unthinkable, but it doesn't kill you.
Meanwhile, Jones has been transported to Boston General, and Olivia goes to visit him. But when she arrives in his room, she finds an enormous hole torn out of the wall -- and a note scrawled on the wall saying "You Passed." Jones has escaped yet again.
Later, Walter reads the manifesto alone in the lab. As he reads, we notice that every lower-case "y" in the book is curiously raised.
Olivia's apartment. Olivia receives an unexpected call from Nina Sharp, who tells her that it turns there was another, much smaller clinical trial of Cortexiphan... in 1981, in Jacksonville, Florida.
In the lab, Walter pulls a dusty tin box from a closet. He opens it to reveal an old typewriter. Walter sets it down and loads a sheet of paper into it. He slowly types one word: "ability." And as the last character appears, he sees it is a curiously raised "y."