Olivia and Broyles are called to a crime scene and find the corpse of a shapeshifter. They discover that the name of the man the shapeshifter was impersonating, Michael Baird, is in Fauxlivia's file. Broyles believes that there is a mole inside their department, tracking down the shapeshifters from the information in Fauxlivia's file and permanently silencing them.
A number of Massive Dynamic employees and FBI agents are made to undergo a high-tech lie-detector invented by William Bell. All suspects are proven innocent, but the team discovers that Dr. Falcon left work early. The FBI storm Falcon's home, but they are too late and the scientist - now revealed as a shapeshifter - has already been killed. When Falcon's body is taken to the lab, Walter finds blood under his fingernails, suggesting that the killer is human.
Narrowing the list of suspects who had access to Fauxlivia's file by blood type, the team come up with one suspect: Massive Dynamic scientist Brandon. However, Brandon takes the lie detector test and is also proven innocent. Meanwhile, a terrified shapeshifter is hunted through the streets and murdered by the real killer, Peter Bishop. Believing Peter to have returned to Massive Dynamic to undergo more tests, Walter is shocked when Nina calls him to enquire about his son's whereabouts. Walter begins to suspect that Peter is the killer and confirms his suspicions by entering his son's bedroom, finding a copy of Fauxlivia's file with the names of the murdered shapeshifters highlighted.
At Walter's lab, Olivia overcomes her unease and reads Fauxlivia's file. She manages to crack her doppelganger's code - a system based around their shared childhood nickname 'Olive' - and uncovers the name of the final target, Zack Alpert. Meanwhile, Peter hunts down and kills Apert, but is interrupted by Walter, who has also tracked the shapeshifter down. Peter explains that he has been killing the shapeshifters to retrieve their data disks, in an attempt to learn more about Walternate's machine, but Walter is shocked by his son's cold-blooded actions. Olivia and Broyles arrive at Alpert's home sometime later, but Walter and Peter have vanished, leaving the shapeshifter's corpse behind.
That night, Olivia is frustrated that the killer completed his mission and that their identity remains a mystery. As she departs the Bishop home, Walter shares a terrifying theory with his son. He believes that just as Peter activated the machine, so the machine has triggered something in him, turning him into a weapon.
Back at Massive Dynamic, Brandon explains to Nina that he has tracked down three copies of a book about the First People - the ancient race who originally constructed Walternate's device. While conducting his search, Brandon has learned that William Bell tried to track down the same books several years earlier. As the episode concludes, Peter stares darkly into his bedroom mirror, his face superimposed with an image of the mysterious machine that is now controlling him.