12. .exe

Fusco discovers that the missing persons he found in the tunnel as corpses have been discovered by the police and is kidnapped by Agent LeRoux, who reveals himself to be the killer. As Finch prepares to deploy his stolen computer virus (named ice-9.exe), he's hesitant because it will also destroy the Machine, so the Machine shows him a series of simulations of what would have occurred to each of the team's members if the Machine had never existed. Reese and Shaw are given a new number: one of John Greer's aliases along with coordinates to Fort Meade, where Finch has infiltrated the NSA and uploaded his virus onto the NSA's Intranet but is captured before he can activate it.

Greer tells Finch Samaritan's wish to rule the world together with the Machine. When Finch refuses to join, Greer sacrifices himself in an attempt to kill Finch by having all the oxygen removed from the room. Reese and Shaw infiltrate the building and activate a wireless modem to give the Machine access within, allowing it to save Finch's life. Finch confronts Samaritan and, with the Machine's encouragement, activates the virus.