Let's catch up with Mr. Jones, shall we? He's escaped from prison via teleportation, remember, and after some R&R in a hyperbaric tank, is ready to wreak some havoc on Boston via a powder that causes the victim's skin to grow over any orifices, suffocating them. Eww! He shows up at the federal building to give himself up, but says he'll only talk to Olivia. Sanford Harass doesn't like terrorists telling him what to do, so he sends Olivia on a raid and opts to talk to Jones himself. This winds up costing him a thousand-dollar watch and the life of an agent, and I can only imagine he's more upset about losing the former. Anyway, Jones leads Olivia to some information about the "multiverse" and there's a lot of mumbo-jumbo about another universe and ours fighting it out to see which one sticks around. The Fringe team learn a little bit about Jones' group with the help of an old manifesto, dug up by another one of Peter's shady connections, about science and technology and mankind being on the brink of catastrophe.
Jones is recruiting those who are worthy enough, which he determines through tests. The first one, for Olivia, is being able to turn off a bunch of little light bulbs -- with her mind. The catch is that she needs to pass the test in order for him to help her prevent a bomb going off that will scatter the orifice-covering toxin all over the damn place. Olivia can't do it, and gets Peter to program the lights to turn off to fool Jones. People, the man teleported out of prison. He's not an idiot.
He seems to fall for it, though, and gives Olivia the location of the bomb. Only when she gets there, she sees the timer is connected to another array of lights that she must turn off with her mind to defuse the bomb. So she thinks really hard at them, Peter cautiously behind her, and turns them off with seconds to spare, although she's not at all sure how she did it.
The teleportation is taking an unexpected toll on Jones' health, or so it would seem. Only he gets transferred to the hospital and promptly rips a hole in the wall and escapes. They do good work at that hospital.
Oh, and Walter wrote the manifesto. Or, at least, Walter's typewriter was used to write it.
So we're back at Science Prison in Germany, and not only are we back there, we are back in time, because there's Mr. Kohl strolling into a meeting room with Mr. Jones, saying he's got Jones' appeal papers all ready to go. Jones is sketching an angular Olivia Dunham, and she appears to have lizard eyes, while Kohl says the best Jones can hope for is life. Jones eventually gets up from his sketching to snap Kohl's neck. He then dresses himself in Kohl's clothes and goes to stand in the corner -- not to give himself a timeout for murdering someone, but so the bright light can fill the room and transport him all the way to Boston.
Meanwhile, back at Science Prison, the guards are going crazy, running through the halls and whatnot, even though no one is yelling schnell!. An officer tells the prison warden (in German, thankfully, and not plain ol' English) that the facility is locked down and all the protocol was followed, so they don't know what happened, other than the prisoner being gone, leaving a scorched corner of the room and a dead body behind.
Two weeks later at Harvard, Olivia wanders into the Fringe lab, where Walter and Peter are already hanging out, like maybe they LIVE there now, and Peter's bringing breakfast to his dad, who is busy washing the underside of that cow Gene that is sometimes there and sometimes not.
In kind of a clunky expository scene, Olivia explains that the German authorities came to see her last night, because Jones escaped, and they don't know how; it doesn't make any sense. "How come when nobody knows and it doesn't make sense, they come to us?" asks Peter. Because if they knew what happened and it made sense there would be no need for an explanation. That's why.
Anyhoo, Jones had been working with Loeb. "I remember Loeb. That's the guy that stole my invention," gripes Walter. That's how he remembers Loeb, and not because he was recently arrested after walking through bank walls and kidnapping Olivia and ordering his wife to kill Olivia. She says she's going to talk to Loeb right now. "But can you describe again to me what you made?" says Olivia, who A) I don't believe would forget about a TELEPORTATION DEVICE, and B) we've been informed has a brilliant memory anyway. Peter tells Walter not to "sugarcoat" it this time, and Olivia asks if it's something that could have helped Jones escape. What, a transportation device? How would that be any help? Walter called it "Disrei," combining "disintegration" and "reintegration." Peter explains it was a teleportation device meant to travel through time.