Season 2 opens with Pierce assigned to determine the mental competency of a man slated to be retried for murder. Unexpected and stunning developments soon mark the trial, which is prosecuted by Moretti's soon-to-be ex-husband.
Pierce and Moretti investigate a woman's claims that her husband was abducted by aliens, only to make an alarming discovery. Elsewhere, Pierce's relationship with his girlfriend heats up, but his imaginary girlfriend could threaten the romance.
Pierce investigates abnormal neurological reactions ailing a group of girls. Soon, he uncovers a dark secret that may be at the root of their condition. Elsewhere, Moretti suspects that Pierce may have hidden motives for working on a case without her.
Pierce and Moretti venture into virtual reality to investigate the murder of a man who obsessively played a multiplayer online game, causing the line between reality and fantasy to blur even more for Pierce.
Pierce receives a tip that the CIA might be assassinating U.S. citizens, a development that turns more complicated when Pierce's close friend is murdered. Meanwhile, Moretti confronts her trust issues with Donnie.