Perception: Season 2

Pierce is asked to be an expert witness in a trial against a biker who is facing the death penalty for torturing and murdering his wife. The District Attorney prosecuting the case is Donnie, Kate's soon-to-be ex-husband. After examining the biker, Pierce comes to the conclusion that he is psychologically a completely different person. Meanwhile, Pierce has begun a relationship with Caroline, however she wants to keep it a secret as he was a patient of hers.

Pierce and Moretti take on an extraterrestrial case when a woman reports that aliens have abducted her husband. When Pierce and Moretti arrive to investigate, however, they make a startling discovery. Meanwhile, things heat up between Pierce and his real-life girlfriend, Caroline, but his relationship could be jeopardized if he can't get his imaginary girlfriend, Natalie, out of his mind.

A judge is murdered during a court hearing. A referee is stabbed in the middle of a basketball game. No one claims to have seen the killings happen. Pierce believes that the victims are somehow connected, but the rest of the FBI, save Kate, are putting their money on the theories of a behavioral analyst.

Pierce accepts an invitation to work on a case from a renowned environmental activist concerning a chain of abnormal neurological reactions in a group of young girls. However, upon examining the girls, Pierce discovers that a dark secret is at the root of their ailments. Meanwhile, Kate questions Pierce's motives in working on a case without her.

Pierce and Morretti plunge into virtual reality to solve the murder of Kurt Simpson, a man who spent most of his time in a massive multiplayer online game called Caleidoscope. After creating an avatar of himself to investigate the crime, Pierce struggles more than ever to distinguish between reality and fantasy.

Pierce and Donnie work together after a brain device meant to control tremors seems to be defective with multiple reports across the nation. When a doctor agrees to talk with Pierce and Donnie, he is later found dead with his wife in a coma. The two must determine if the corporation making this product is to blame, or if something more is going on. Meanwhile, Max dates a Brazilian girl whom he is trying to help get a scholarship.

When Moretti receives a deathbed confession about the hit-and-run murder of a teenager from 1992, she calls on Pierce to determine the ailing man's credibility. The case becomes complicated, however, when the alleged killer's physician, Dr. Hutchins, reveals that his patient’s tumor has mysteriously disappeared. Pierce and Moretti must dig deeper into the past to uncover the truth behind a shocking series of apparent homicides.

Pierce is called to look into a stabbing at a psychiatric hospital; while in a series of hallucinations, Pierce realizes there is something dark going on in the hospital.

Pierce is asked to look into the case of a war hero that exhibits violent, erratic behavior and realizes she has a neurological disorder from contracting herpes. Later she is accused of murdering a former platoon colleague and it's up to Pierce and Kate to prove her innocence. Meanwhile, Pierce's college girlfriend returns to teach for a semester.

Moretti faces criminal charges after taking things into her own hands while working on a dangerous case. Pierce and Donnie strive to clear her name, but as conflicting evidence builds, even Kate begins to question her own innocence. Donnie and Kate gets closer together.

Pierce helps out when an autistic teen is under investigation for murder with help from his hallucination Hall of Fame Mordecai "Three Finger" Brown. Dean Haley sets out to convince a neuroscience prodigy to attend CLMU.

Lewicki's brother, Kenny, makes a surprise visit. When he's later named as the suspect in a murder, Pierce's loyalties are torn between friendship and justice. An enticing offer makes Lewicki question Pierce's loyalty to him.

Tensions arise between the CIA and FBI after Pierce receives a tip that the CIA might be assassinating U.S. citizens. Things become more complicated when one of Pierce's close friends is murdered. Meanwhile, Moretti tries to overcome her trust issues with Donnie.

Pierce's mental stability is questioned and his job threatened when he is accused of stalking his ex-girlfriend, Caroline Newsome. As the situation escalates, Moretti works to find the real stalker with help from a visiting inspector from Canada.