Once she's gone, Peter goes back to being cocky, congratulating Walternate on his brilliant performance. Well, if the Emmys aren't going to do it... "You almost looked genuinely surprised to see me, which we both know is not the case," says Peter.
Walter, opening up some kind of case and assembling a multi-pronged handheld device, admits that he's known about Peter for some time: "I've been monitoring the intelligence feeds from the other universe," he says. "Yeah, if by 'monitoring' you mean 'spying,'" says Peter. Well, of course that's what he means, Peter. Don't be such a baby.
Peter says he knows Walternate already tried to have him killed once today, and Walternate, admitting nothing and actually seeming a little amused, asks why he would do that. Peter suggests Walternate sees him as a threat (because Peter's so bad-ass) and says the other side knows Walternate has been sending human shapeshifters into their side, in violation of the accord.
So you have come all this way to bring me to justice," says Walternate. Yeah, it's ludicrous, obviously. Peter's still on his whole "it's not my fight" routine, though, and says all he wants is Walternate's help to get back home: "If you want to get rid of me, just help me," he says. By this point, Walternate's standing in front of Peter, holding the little mystery device.
Walternate says that if Peter believes these awful things about him, then his decision to come here must've been difficult. Peter thinks about it for a long moment, and says, "I didn't really have any other choice." Walternate, half-smiling, says no one knows more about the burden difficult decisions than he does.
That's when Brandonate comes in, saying Sgt. Kane said Walternate wanted to see him, and he is practically yelling at the top of his lungs for some reason, and Walternate explains that Peter is from the other side and is accusing him of sending shapeshifters over to the other universe, murdering innocents, canceling beloved television shows, that kind of thing. "Now, you are my chief scientist. You know me and my operation better than anyone. Is it possible? Is there any way that what he is saying could be true?" Brandonate thinks about it for a moment, then says he doesn't see how, and Peter greets that with the smirk it deserves. Brandonate dresses it up a little bit, saying that he examined the shapeshifter tech in detail and saw nothing to indicate Walternate had anything to do with it. "There, you see?" says Walternate to Peter, and the two stare at each other for a moment, just before Walternate fires his little doohickey right into Brandonate's chest, sparking and whirring, causing him to collapse, his face morphing and shifting. Walternate turns back to Peter. "Not everything is as it seems," says Walternate.
When we get back after a commercial break, an unconscious Brandonate is laid out in some sort of lab, all manner of tubes sticking out of him. I have to admit, I'm a little curious about how Brandonate was moved from Walternate's multi-windowed office to this lab without any apparent problems. I mean, even for the Secretary of Defense, that's a neat trick. I'm going to assume that they stuck a hat and sunglasses on him and, Weekend at Bernie's-style, walked him down to the lab with no one the wiser. Anyway, Walternate tells Peter that he'd suspected for some time that Brandonate had been replaced by a shapeshifter, so he had his men follow him, monitoring his communications. He says he's going to interrogate him. "Earlier today, a State Department employee was the victim of another shapeshifter, trying to acquire his identity. It's become all too clear that elements of our government are being infiltrated," says Walternate. Peter asks, not unreasonably, why, if Walternate's known about this for so long, he hasn't done anything? Walternate says if word got out that elected officials and other authorities were not who they claimed to be, it would cause widespread panic and society would collapse. I don't know. I think the public is getting pretty used to elected officials not being who they claim to be.
Anyway, Peter says he's got to find the shapeshifters and expose them, using that little thingy he used on Brandonate. Walternate points out that he spent weeks convincing himself that Brandonate had been replaced; if he'd been wrong, and Brandonate weren't a shapeshifter, the tech would have killed him.
Peter wants to know why Walternate is telling him all this. "Because you are the only person I can trust," says Walternate. Again, given that you managed to get the body of your chief scientist out of your office and down to this lab, I gotta figure Walternate's got more people he can trust than just Peter here, but let's go with it. Walternate's logic is that Peter has no alliances to their side or the other, and he needs Peter to deliver a message.
Peter starts to protest, saying he appreciates what Walternate's up against, but -- "It's not your fight?" says Walternate. See, even Walternate's sick of hearing Peter say that. Peter says the Walter on the other side refuses to help, but Walternate understands the machine and -- AGAIN -- is the only person who can help him get back to where he belongs. Walternate says he'll help, as long as Peter first goes back to the other side and tells them that he's not their enemy, and whoever is behind the shapeshifters is a threat to them all. Peter stares at him -- I was kinda hoping he'd do that Larry David thing where he gets up close to a person to try to tell if they're lying -- and then, with just a trace of emotion, says he was wrong about Walternate: "You're not the man I thought you were." Walternate smiles and says Peter is exactly the man he thought he would be. Mouth quivering slightly, asks Peter to help them.
Over at Fringe Division, Fauxlivia tells Lincoln Bee that the Farnsworthbot traced the call to an industrial park in the Flatiron district, which has been abandoned "since the amber riots of '06." Lincoln Bee says that doesn't sound like it's connected to the Department of Defense or Walternate -- because Walternate wouldn't be smart enough to issue a kill order from a phone that couldn't be traced back to him, I suppose? Smarten up, Lincoln Bee! God! -- but Fauxlivia wants to check it out anyway.
Lincoln Bee wants to know how much longer they're going to keep Col. Broyles in the dark: they're chasing the story of a suspect who may have murdered two Fringe agents, and who they've got locked up in a broom closet instead of Holding, where he belongs. Yeah, about that -- how is it that no one at Fringe DOESN'T wonder what the hell is going on? It's not like Fauxlivia and Lincoln Bee arrested Lincoln Lee on their own. Anyway, Lincoln Bee figures they have to tell Broyles something.
So they go to his office, where Col. Broyles asks if they processed Lincoln Bee into Holding. Lincoln Bee doesn't technically lie when he says, "He's been secured, sir," and before that story can be questioned, Fauxlivia jumps in and says that's not why they're there. Col. Broyles looks up and then asks them if it's about the trace they ran on Agent Murphy's ear cuff. Fauxlivia and Lincoln Bee look momentarily surprised to find out they're not super-smart ninjas running rings around the rest of the morons here, and Col. Broyles says the Farnsworthbot told him. He asks what they're looking for.
"It may be nothing, but until we know more, we would like some leeway on this," says Fauxlivia. Col. Broyles sighs and agrees, telling them to keep him posted.
Fauxlivia and Lincoln Bee leave Col. Broyles office, and then there's a long shot of Col. Broyles watching them go, television standard for "We're about to reveal this guy