When Donnie finds himself in a compromising situation, he calls Pierce for help. As the evidence begins to stack against Donnie, Pierce and Moretti struggle with their own fears and doubts, as they work to solve the case. During the chaos, Pierce must deal with his father after he assaults someone at the assisted living facility.

After Pierce witnesses a gallery owner die during a seizure caused by a video installation, he convinces Moretti that it was actually a murder. Their search for the killer puts them in the middle of a brazen art heist. As Pierce works on the case, he is forced to re-examine his relationship with Natalie.

After a missing FBI agent turns up dead, Pierce is forced to face the one case he was never able to solve. When they discover that the killer is still out there, Pierce agrees to help Moretti, against the wishes of his therapist, Dr. Rosenthal, who believes it will only exacerbate Pierce’s condition.

Donnie and Moretti are caught in the crossfire when a sniper shoots up the lobby of the Federal Building. When Pierce determines that the shooter is afraid of Extreme Low Frequency radio waves, he and Moretti take a trip to the Quiet Zone in Virginia, where they think the shooter is hiding out. Meanwhile, an alluring woman named Shelby Buchanan courts Donnie to run for political office.

A student tips off Pierce about a potential conspiracy to cover up the murder of a U.S. Senator.

Moretti learns that there may be some truth to Pierce's conspiracy theory; Pierce's new doctor forces him to face the truth about Natalie.

Pierce fights for an autistic teen who is under interrogation for murder; Dean Haley attempts to convince a neuroscience prodigy to attend CLMU.

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.

When an infant is reported stolen, Moretti hunts down the kidnapper and makes a very bizarre discovery. As Pierce and Moretti investigate a related murder, they find that there might be another child out there who needs their help. Meanwhile, Donnie and Moretti discuss their future together when Donnie looks into buying a house in the suburbs.

Pierce investigates a stabbing at a psychiatric hospital and becomes convinced that the hospital is full of dark secrets.

FBI Agent Kate Moretti asks Dr. Daniel Pierce to determine the mental competency of a man being retried for murder. But the trial takes a shocking and unexpected turn when Pierce’s findings question whether the person standing trial is the same person he was six years ago. Meanwhile, Moretti is unpleasantly surprised to discover that the Assistant U.S. Attorney prosecuting the case is her soon-to-be-ex-husband Donnie Ryan.

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.

When a series of bizarre public murders occur, Pierce realizes that the killer is trying to send a message about inattentional blindness, but Donnie doubts this theory. But Pierce has a trick up his sleeve that can prove his point, and they must scramble to piece together the clues before the clever killer can make any more examples out of innocent victims.

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, Moretti 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 receives a tip that the CIA might be assassinating U.S. citizens; one of Pierce's close friends is murdered; Moretti tries to overcome her trust issues.

When a prosecutor mysteriously drops dead in the middle of a courtroom, Pierce and Moretti go on the hunt for a killer. Meanwhile, Moretti and Donnie make some decisions about their future.

Moretti calls on Pierce to examine Elena Douglas, a woman who has confessed to murder and claims to be possessed by the Devil. Meanwhile, Donnie and Moretti’s wedding plans hit a bump in the road.

Agent Kate Moretti goes under cover to investigate an animal rights group suspected of foul play; Pierce considers making a confession to Kate.

When a student is found murdered, Pierce tries to find the killer while defending the victim's boyfriend; Pierce must confront his feelings as Kate and Donnie prepare for their wedding day.

When Moretti goes missing the day of her wedding, Pierce and Donnie set off in pursuit of the runaway bride. They soon learn that Kate has been abducted by a dangerous person from Pierce's own past. Now, Pierce and Donnie must risk everything to save Moretti before it's too late.

Pierce tries to crack a coded message left in a newspaper by someone who may be connected to a murder. But time isn’t on his side as another victim’s life could be in danger.

Pierce and Moretti race to find clues when a serial killer from 1986 begins killing again. They catch a break when they learn that one of the victims is actually alive. Moretti's dad, one of the investigators on the original case, offers his daughter advice. Pamela Reed also guest-stars as the mother of the surviving victim, while Armin Shimerman is the victim's psychologist.

When a young man in a cult claims to be hearing the word of God, Pierce must determine if it’s actually the word of God or a life-threatening neurological condition. Pierce and Moretti must also figure out if his murder is linked to his drug past or his new life with an organization that may be scamming people out of their life savings. Roger Bart guest-stars as Ethan Kendrick, a high-powered IRS agent looking into the finances of the organization. Meanwhile, the university gives Pierce an award for his research.

Pierce must take a deep look into his own life when he is brought into a case involving a schizophrenic. Meanwhile, Moretti stops at nothing to impress her new boss at the FBI. Guest star Tom Sizemore plays a top-level Irish mobster, while guest star Edward Furlong plays a would-be tough guy who may have played a crucial role in the crime.