Flashback to Wissenschaft Prison, Germany, as Jones's lawyer comes to visit, bringing Jones his sunscreen, etc., etc., and ending up dead on Jones's cot as the prisoner teleports out of the cell and into Boston.
Two weeks later, Olivia tells the Bishop boys about Jones's escape from prison. She's heading off to interrogate Mitchell Loeb again and wants Walter to remind her what it was he (he who? Walter? or Loeb?) was working on. Walter says her that it was a teleportation system. Color Olivia intrigued. Meanwhile, over at Jones's top secret hideout, he emerges from the decompression chamber he's been in for the past two weeks. He asks a flunky if everything is ready. It is. Jones has a case of the shakes, however.
A man wearing latex gloves gives a newsstand vendor a $2 for a paper, not waiting for his change. Shortly thereafter the vendor's eyes, nose and mouth start sealing up, the skin growing over them. Other customers scream in horror as the man suffocates right in front of them.
Prisoner Loeb is brought to his meeting with Olivia. She wants to know where Jones is. "You're not someone I really want to work with," gripes Loeb, no doubt referring to the fact that Olivia shot his wife dead not too long ago. Olivia threatens him with a transfer to a Very Scary Prison but Loeb remains resolute: what was written will come to pass and nothing Olivia does will stop it. She is interrupted by a phone call from Broyles, telling her to collect the Bishops and go to MGH.
At the hospital, Walter examines the vendor's body. Olivia makes the assumption that Jones is behind this attack but has no proof. She speaks with Peter outside, saying that the initials "ZFT" that keep popping up in the investigation may refer to a manuscript about "destruction through the advancement of technology." The one known copy was thought to have been destroyed but she's hoping that Peter might be able to use one of his "weird connections" to find it. Peter's like, you're weird ... but let me try.
They take the vendor's body to Walter's lab, which makes Astrid concerned that it might be contagious. Walter says no, not to worry, and pokes a hole in the flesh covering the vendor's mouth, siphoning out the gas trapped within. Astrid chokes at the smell.
Peter and Olivia stop by an indie bookstore, asking about the manuscript. The bookseller will look into it.
Charlie's teams has found a warehouse in Allston, leased to Jones's (now-deceased) lawyer, that recently had its power turned back on. Before Broyles can send a team to investigate, however, Jones himself shows up in the FBI HQ lobby. They put a gun on him and he raises his hands, saying calmly that he will only speak to Olivia. They take a key off him and send it to Forensics. Harris is not inclined to acquiesce to Jones's demand and instead sends Olivia to investigate the warehouse without speaking to Jones. If she can come up with hard proof that he was connected to the dead news vendor, maybe he'll let her talk to him. Meanwhile, Peter's bookseller has procured a copy of the manuscript. Peter reads some of it to her over the phone and it's all dark and dismal and about technology bringing about the apocalypse. Keep reading, says Olivia.
When the FBI team gets to the warehouse, they find the decompression chamber, a sketch Jones did of Olivia ... and a folded $2 bill. Of course, the poor kid who found the money gets his face grown over and starts to smother. Olivia does an emergency tracheotomy but that hole grows over too. The agent dies.
While Olivia is thus occupied, Harris tries to interrogate Jones. Jones doesn't want to talk to anyone other than Olivia - he's not that well and is hoping to avoid "any more unnecessary deaths." He also gives Harris a list of things he'll need when Olivia meets with him: walkie-talkies, analog wristwatch, etc. Olivia goes to the interrogation room upon her return, handing Jones the stuff he asked for. He quickly tinkers with it and manages to put together a device that disrupts all the audio equipment in the room, allowing him to speak privately with her. He admits that something far worse is coming than what is currently going on but first he wants Olivia to pass a test. He tells her to take that key and go some place to fetch something he's left for her there. She has sixteen hours before an explosive detonates that will kill hundreds of people just like the agent and the vendor. She takes off.
Walter reads an excerpt from the manuscript in voice-over as Olivia retrieves the box left for her: there are other worlds besides our own, and there are those who have already found the passages between them, and only one world will survive - it's us or them. Back at the lab, the box is full of puzzles/tests. Olivia is to take the first one - turning off a series of lights using only her mind - and get back to Jones. She's skeptical, of course, but gives it a go as the Bishops and Astrid watch. Her phone rings: it's Charlie, saying they've got a hit on the van carrying the explosive. She hangs up the phone and grabs her coat, refusing to play Jones's "mind game."
Olivia tells Jones that he's got some insane delusion where he thinks he's recruiting her as a warrior in some imaginary war - she doesn't want to play. Jones says that she's already part of it, having been treated with some chemical compound via spinal tap. He's insistent that she take his tests but collapses in pain. They take him to Walter's lab for patching up. Olivia says that she has to go to Massive Dynamic to find out about that chemical compound (she can't use the phone?). In the meantime, could Peter maybe rig that lightbox so she can fool Jones?
At the Massive Dynamic offices, Nina Sharp confirms that cortexyphan was created by Walter's old lab partner, William Bell, in 1981. It was meant to be administered to children to limit the eventual limitation of the human brain, Bell having believed that each human is born with limitless potential but that the potential shrinks with age. The drug was apparently only run in trials in Ohio. Olivia points out that she never lived in Ohio - she grew up on a Jacksonville, Florida, military base with her family.
Back at the lab, Walter has revived Jones (who is in rough shape). Olivia tells him that she can pass the test - because Peter has successfully reprogrammed the light box. She demonstrates and Jones apparently buys it, telling them where the bio bomb is going to be: on Church Street in Boston. [I used to work on Church Street in Boston, btw.]
Excellent: when they find the bomb, the bomb squad can't defuse it because they don't understand the wiring, which is identical to the light display on Olivia's test box. She calls Jones at the lab, confessing that she faked it before. He says he knows, but he believes that she is capable of actually doing it, turning those lights off with her mind. He has faith in her: there is only one way out of this and it's her.
Olivia stands in front of the bomb, one minute left. Peter tells her that she's nuts and he can't stay to do this with her. He heads for the elevator with the rest of the team but turns back at the last moment, coming to stand quietly behind her. Olivia stares at the lights, calming herself. And slowing, one at a time, the lights out out, all of them, with two seconds to spare. Peter is incredulous: how did you do that? Olivia is trembling: I don't know.
Afterwards, she has convinced herself that it was still a mind game, programmed to turn itself off. Peter's like, okay, I didn't die tonight so I'll believe anything you want to tell me. He asks if she wants to go get a drink, or five, but she's going to MGH where they've just transferred Jones. She has a few more questions for him.
Walter and Astrid are cleaning up the lab and she tells him that she thinks his having invented a teleportation machine is pretty damn cool, despite the fact that it kills you if you use it. Walter says she's mistaken: it does something unthinkable, but it doesn't kill you.
When Olivia gets to the hospital, everyone is in a tizzy because there's a huge hole busted through the wall in Jones's room ... but no Jones. There is a message for Olivia, however, written on the wall: YOU PASSED. A little later, she gets a phone call from Nina Sharp who has uncovered a second, smaller clinical trial for cortexyphan, down at a military base in Jacksonville, Florida. Dun dun dun dun!
Walter continues to read the manuscript later: what we think of as reality is a larger multiverse. He frowns, looking at the Y in "reality," which skips a little, riding higher than the other letters. He digs an old typewriter out of a closet, inserts a piece of paper and types "ability." The Y in that word is the same as the Y in the manuscript. Walter wrote the manuscript.
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