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Broyles, Walter, Olivia and Peter go the military site where Nina Sharp and Massive Dynamic are building the machine. When Peter arrives, he triggers the device in a way they had not yet been able to do.
Massive Dynamic conducts electromagnetic testing on Peter to see if it was truly he who affected the machine, while Walter worries and wishes for Nina to help him fix the brain cells William Bell inhibited so they can replicate again, and he can be smart enough to think like Walternate. Nina gives Walter an antidote William made in the event Walter wanted his brain back. There were three vials, and Walter just sniffs unabashedly. He later begins having the mannerisms of a chimpanzee.
Many tests are done on Peter and there is no indication of his affecting the machine. Until the doctor in charge of the tests looks strange, we almost believe him. He is later found, dead. A shapeshifter.
Another dead body is found, another shapeshifter. His data storage was removed and they think perhaps Walternate has sent cleaners to scrub whatever information Fauxlivia gathered while she was in our universe. Her computer has been cracked and Broyles asks Astrid to filter through it. Because the information reads like a diary, they do not want Olivia involved.
The strain between Olivia and Peter is palpable. She wants to help with the files, but Peter thinks that Fauxlivia would portray him in her diary like a fool who had been conned, and he cannot stand the thought of that. Olivia apologizes for not thinking of Peter’s feelings in all of this, and says they can get past it. However, when she reads the diary, Olivia realizes Fauxlivia had real feelings for Peter, and just how much alike they truly are and she deciphers a code being used to destroy the shapeshifters. She later tells Peter he need not feel a fool at the hands of Fauxlivia.
Peter tracks and shoots a shapeshifter, just after it shifted. it is not the first nor is it the last shapeshifter he will track and kill. Walter finds Peter being held by a shifter. Walter watches as Peter chops, stabs, removes the chip and then kills the shifter. He says he is doing nothing wrong, because they are not even human. Olivia calls and tells them they are on the way. Both Walter and Peter have left.