Walter, who is now the owner of Massive Dynamic, finally agrees to allow Nina to begin assembly of "The Vacuum"-The Machine which Peter is intrinsically connected to. And so Fringe Division is shown driving into a Highly Secured Base where they are assembling The Machine. Walter has to ask the guard if he has any Gum.
This is the first time that we see the fully assembled machine, in all of its glory. We had seen parts of it partially assembled in the season two finale, I had assumed that was a matte painting but they actually had parts of the full machine assembled even back then. To see it here fully assembled is beyond magnificent.
When Fringe Division enters the room, all of the monitors which were dead, start coming to life, The Vacuum knows Peter is There. And so Massive Dynamic start doing all manner of tests on Peter. Walter has a problem with one scientist in particular, "Dr. James Falcon" (Charles Parnell) - Who seems overly eager to get Peter into all kinds of MRI machines.
Astrid is trying to "decode" Fauxlivia's Macbook Pro: Peter had guessed her password, but the data is in one huge file. Olivia offers to help, but she is kept away because Broyles, Walter, Peter and Astrid feel it would not do her any good to see what Fauxlivia had written.
But Shapeshifters are showing up dead with their "Hard Drives" removed. And Peter is shown, coming in very late at night, and lying to Walter about it. Does he have anything to do with this?
Mainly this episode pieces together some apparently unrelated fragments: Shapeshifters, The Machine, Fauxlivia's Macbook, etc... and Walter is concerned for Peter's state of Mind after being exposed to The Vacuum, is it "Weaponizing" him?
It is Peter who is killing the Shape-Shifters and taking their disks. Olivia finally just grabs Fauxlivia's Macbook and starts reading it, it is not as "bad" as her "protectors" thought. In fact, it is a written a lot like Olivia would write it - Fauxlivia makes sense of things exactly as Olivia would, and this allows Olivia to find a code hidden in the file, which gives the names of five Shape-Shifters.
Walter has figured out what Peter is up to, and he follows Peter to the house of the Last Shape-Shifter, who had laid a trap for Peter. But Peter gets the drop on the Shifter when Walter walks in the door, chopping off the shifter's fingers with a Butcher Knife. Mercury Splatters Everywhere. Peter explains to Walter that he is through being "reactive," he wants to be pro-active, so he began a collection of Shifter Hard drives. As he shoots the Shifter in the head, he tells Walter, "I'm not doing anything wrong, these things are not even human."
Walter thinks Peter's exposure to The Machine has changed him into something he was not, and as this episode ends, Peter is sitting alone in a room while an image of The Machine looms in an overlay behind him.
This leaves us with the question: Is Peter being Changed into something Bad?
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