Picking right up where we left off, Peter takes the call from that janitor lady Olivia tasked with informing him that he's sleeping next to the wrong Olivia. Accepting the news pretty immediately (we always knew he kind of knew there was something off about Fauxlivia, right?), he silently wigs out and starts going through Fauxlivia's enormous and unwieldy MacBook Pro with a Windows OS, because Fauxlivia lives dangerously. She catches him, and he tests her with the Greek phrase Olivia said to him way back when, and when Fauxlivia asks him where he heard it, he knows the truth. But she does too -- she pulls a gun on him, forces him to inject himself with paralysis juice and heads out with the laptop she thinks is hers, but since they have identical MacBook Pros with a Windows OS (WHY?), she takes the wrong one. Also, Peter's eyes are open and he's going to be paralyzed for "a few hours." He's gonna have prune eyes by then!
Fauxlivia goes up to that typewriter place in the Bronx, tells the other side her cover's been blown, and gets instructions to go down to Penn Station to prepare to crossover. Through a series of events that involve pastries and Walter cursing Olivia for tricking Peter with her feminine wiles and "vagenda" (an underused term), the Fringe team tracks Fauxlivia to first the typewriter shop, then Penn Station. The Penn Station is the Newark, NJ one, though, which is not explained, but whatever. Recreating midtown Manhattan is expensive to do in Vancouver, after all.
Back in the other world, lab geek Brandon has convinced Walternate to send Olivia back dead, but with key organs missing so he can study them. Olivia quickly figures this out and appeals to Alt-Broyles to help her, and though he refuses at first, he eventually decides to bust into the surgery room, shoot Brandon in the face, and save Olivia. When they discover the Deprivation Tank has been drained, they steal a buttload of Cortexiphan and take off for Walternate's old Harvard lab, fill the Deprivation Tank there with water and rock salt, and Olivia gets in and teleports, just as the whole damn army comes in to intercept them. Olivia wakes up in our Harvard lab, scares the shit out of Astrid, passes out and is home forever now! Yay!
When Fauxlivia gets to Penn Station (which is called "Springsteen Station" in her world -- Jersey joke! Chortle, chortle!) she is greeted by a handsome shapeshifter who injects her hands with something painful in the ladies room. When a woman comes in and interrupts them, they walk out to find the Fringe Team encroaching on them, guns drawn. Fauxlivia fires at them and retreats back to the bathroom, only to come back out with the woman who interrupted her before as a hostage. The woman's daughter runs up behind screaming "Mom! Mom!" and when Peter asks the woman three times what her daughter's name is and doesn't get an answer, he shoots her in the head because IT WAS THE SHAPESHIFTER OMG PETER IS A GENIUS. Fauxlivia looks hilariously buzzkilled at her getaway plan being foiled. This show is so awesome.
Outside, Fauxlivia is waiting in a paddy wagon, handcuffed, while Peter and Fringe team get the call that Olivia is back, and recovering at the hospital. Before they can celebrate, Fauxlivia's injected palms start glowing bright red, the paddy wagon starts a-shakin', and she teleports back to the other side, leaving in her place the mutilated (and incomplete) body of poor Alt-Broyles, who must have been killed for helping Olivia and put in The Tank. Poor guy. I know I'll certainly miss the superior Broyles on this show.
At the end, we see the typewriter shop guy sitting at a table with a creepy man in a red sweater. At the beginning of the episode we learned that the typewriter clerk has been helping Fauxlivia because The Other Side had promised him new legs (he walks with crutches), and now we see him getting them... in the form of some crazy injection. He quickly gets up and starts walking free of crutches, and the red sweater man takes in exchange a piece of The Device that Fauxlivia had stolen from Walter to bring back to Walternate. That thing's going to explode the universe this spring, y'all.
So we get a replay of the phone call that Peter gets (gotta get that extra cellphone product placement in) from the woman telling him about the disappearing Olivia from another universe. And then a sleepy Fauxlivia asks him who was on the phone, and he pretends it was a telemarketer, which seems kind of dodgy at midnight, but Fauxlivia just says he should save their number and call back when they're sleeping.
And then Peter lies awake (I presume) for the next couple of hours, and we watch a digital clock change instantly to 2:15, and it would be kind of cool every so often to get the old speeded-up-clock-hands effect that movies and television used to use. I know, it seems cheesy... Anyway, Peter gets up while Olivia sleeps, and skulks around, opening a dresser drawer and inspecting Olivia's stuff -- notepads, files ... he finds a strip of photos of the two of them together, the kind you get taken for a couple of bucks in a booth at the mall. He looks at it for a few moments, and then spies the two Mac laptops on the nearby table, which have identical screensavers running, and he picks hers up, and it's one of those Mac laptops that uses a Windows operating system for some reason.
He starts going through the files -- old Fringe cases -- and tries unsuccessfully to get into a locked file that accepts none of the passwords he attempts. Try "Eric Stoltz in Back to the Future"! And then suddenly Fauxlivia's there, asking him what he's doing up. "Just sending an email," he lies, and she's all, "At 2:15?" and he points out that "it's not 2:15 in Greece," and she doesn't point out that an email is not the same as a phone call, probably because she figures that Peter, not being a moron, should know that. He tells her he has a friend in Corinth. "And like he always says..." and then Peter repeats that Greek phrase that I won't even try to transcribe, the one that Olivia blurted out when she returned from her first trip to the other universe.
Of course, Fauxlivia has no idea what it means, and so then the soundtrack gives us the big bass note of betrayal, but he recovers enough to say, "It means, 'be a better man than your father.'" And then Peter makes up a story about his friend's father. Fauxlivia says she's going back to bed, and Peter says he'll be right there, he's just going to get a glass of water. After she leaves Peter gets up and opens and closes a cupboard just for the sound effect. Then he stealthily goes back into the living room, but her gun that was on the table isn't there anymore. She's got it, and she's pointing it at him.