Peter has a revelation in a dream and goes to visit a startled Walter, who's investigating changes in the laws of physics. Peter implores him to help reconfigure the Machine's temporal matrix. The laws of physics are changing because he's here, and things will only get worse if he doesn't leave. Walter sadly recalls Elizabeth's suicide. He lost his wife, his career, his sanity - and damaged two universes - by trying to help another Peter. So, no. He can't help.
Peter visits Olivia, who's home with a migraine. He wants to use the bridge to cross to the Other Side, hoping that Walternate will help him. Olivia protests, because Walternate is a bad guy who's been sending shapeshifters to their side. Besides, how would Peter get into their Department of Defense?
Lincoln arrives, and Peter realizes that they can disguise him as his Other Side counterpart to get into the DoD. Olivia reveals that the portal device Walter used in 1985 isn't submerged in Reiden Lake, as in Peter's timeline. It's Storage Item 317 at Massive Dynamic, which recovered it years ago. Olivia's been thinking about doing some recon. Peter wonders why she needs the portal when she can cross anytime by herself, which just confuses her.
Peter's not OK with Olivia's plan to secretly investigate the human shapeshifters. If they're busted, Walternate will think Peter's involved. Olivia backs down but privately tells Lincoln to carry out her plan.
On Liberty Island, Dr. Fayette brings Walternate the human shapeshifter tech he's been studying. They might be able to trace a signal back to whoever's behind this. Walternate says that he'll do the back trace, over Fayette's protests.
Bolivia and Agent Lincoln Lee investigate a Fringe case at the Battery Park Bus Terminal, where a man with a weirdly messed-up face killed another man, then leaped OVER a bus, but then was killed by another passing bus. Suddenly, DoD troops led by Sergeant Elias Cain kick them out - Walternate's orders. Later, Bolivia tells Lee that she suspects the body was a human shapeshifter. What if Walternate is trying to cover up his involvement?
Olivia, Peter, and Lincoln (now dressed like Agent Lee) set up the portal device at the familiar old Orpheum opera house in Brooklyn. Lincoln is wary, especially when Peter says that if the portal closes while he's going through, he'll be cut in half. Peter once killed a bad guy that way.
Walternate has the shapeshifter's body brought into Fayette's lab, and has Sgt. Cain stand guard as he privately retrieves the disk. Meanwhile, Lincoln arrives at the Liberty Island ferry with Peter as his "prisoner," telling the guard he's lost his Show Me card.
When Agent Lee gets the message that his ID has been reported lost, Lincoln and Peter are busted. Colonel Broyles informs Walternate about the intruders - one of whom claims to be his son. Walternate says, Don't contact the other universe until you've interrogated them.But then Agent Murphy, who's driving Peter and Lincoln in a prisoner transport, gets a call over his ear cuff communicator and suddenly speeds away from the convoy. He shoots his partner, and he is about to kill Peter when the wounded agent shoots Murphy. Peter escapes while Lincoln surrenders to Bolivia and Agent Lee. Saying Walternate has probably infiltrated Fringe Division, he explains about the call to Murphy and suggests they trace it. Bolivia and Lee secretly stash Lincoln in a maintenance closet at HQ while they do that.
At home, Elizabeth Bishop comes face-to-face with Peter, who says that he needs to speak with her husband. Looking at him closely, she says, "Peter?" He gently explains he's not her Peter; he's from another place - and he has to get back there. She says that she always believed that, somewhere, Peter would have a life.
Walternate and Peter meet privately in Walternate's office. As they verbally spar about the human shapeshifters and whether Walternate tried to have Peter killed, Walternate coolly arms a small device with a wicked four-pronged head. Peter insists that he just wants Walternate's help to get back where he belongs.
Dr. Fayette enters, and Walternate asks if Peter's theory that he's responsible for the human shapeshifters could be true. Fayette says he doesn't see how, then begins to ask a question, but - BZZZZTTT! Walternate blasts him with energy from the device. Fayette's body goes all wonky - he's a shapeshifter!
Peter looks at Walternate, who calmly says, "Not everything is as it seems."
Walternate had long suspected the doctor had been replaced. Elements of their government are being infiltrated, and if people find out, society will collapse. But Walternate can't just expose the shapeshifters with his device, because it's fatal to real humans. He can trust Peter, who has no alliances to either side. Walternate promises to help Peter, but right now he must tell the other universe that whoever's behind this is a threat to them all. Please do this for me, says Walternate. Help us.
At Fringe HQ, Bolivia and Agent Lee trace the call to Murphy to an abandoned industrial park in the Flatiron District. Broyles knows this and makes a call to inform someone. That someone is a scarred-looking David Robert Jones - a version of the biochemist/ZFT leader who, as mentioned earlier, was killed by Peter while trying to escape to the Other Side. He's in a warehouse full of shapeshifters in tanks.
At the Orpheum on This Side, Olivia's startled to see September the Observer, a stranger to her, who's been shot in the chest. "I have looked at all possible futures," he says, "and in every one, the result is the same: You have to die." Then he disappears.