Pierce is hired to determine the competency of a convicted murderer who has been granted a new trial. After examining the killer, who had subsequently suffered a brain injury and now exhibits a completely changed personality, Pierce asserts that he is essentially no longer the same person and should no longer be held accountable for the murder. His work puts him at odds with the new prosecutor Donnie Ryan, who doesn't like the fact that Pierce is interfering with his case, or that he is such good friends with Kate, his soon to be ex-wife.
A woman becomes convinced that her husband is no longer really her husband. When it appears she has murdered him she claims she really didn't kill her husband - only his alien impostor.
A series of murders take place in front of witnesses who aren't even aware that someone has been killed. Pierce struggles with getting the FBI to accept his theory of mass blindness while he deals with the interference of a consultant.
Pierce consults on a case in a small town where teenage girls are suddenly displaying symptoms of Tourette's Syndrome. If it isn't from environmental poisoning or a bacterial infection it may be from collective guilt over a tragic incident.
In order to get information on a murder suspect, Daniel and Kate have to go undercover in an online gaming community. But being immersed in an imaginary universe is hardly the place for a schizophrenic like Daniel.
Parkinson patients start dying from defective implants used to control their symptoms. But even as he realizes the “malfunctions” may be a cover-up to murder, he also wonders if the miracle device could be a cure to his schizophrenia.
A man dying from a brain tumor confesses to a 20 year old killing, but then recants when he is suddenly cured. Meanwhile, Daniel begins to see his dead mother, due in part to his guilt over the way she died.
Daniel agrees to help a woman accused of killing a nurse in a state hospital even though it means going undercover inside an asylum. Once he's inside, his own hallucination has to compete against something the patients call “Creek”.
After a decorated war hero is arrested for destroying a convenience store, Daniel believes her erratic behavior is the result of an infection that produced swelling in her brain. Kate convinces Donnie not to prosecute her. After she is implicated in the deaths of two of her fellow soldiers, Kate begins to regret her actions until the soldier accuses a Congressman's son (her platoon sergeant in Afghanistan) of rape. Kate makes it her mission to see that he is brought to justice. However, in her zeal to get him she may go too far and end her career.
In the conclusion of “Wounded”, Kate goes on trial for the death of Sgt. Rickford. Donnie resigns his job to become her defense attorney even though Kate begins to doubt her own account of events and thinks she may in fact be guilty.
An autistic boy obsessed with trains, appears to have killed a security guard when he unexpectedly moved a train. Pierce realizes he actually prevented a railroad collision and that the dead guard may have been the victim of someone else.
Max Lewicki's estranged 16 year old brother shows up at Pierce's house one step ahead of the law. He eventually confesses to a murder but Pierce thinks that he only imagined it and tries to find the real killer.
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.
Pierce's academic career is threatened when he hallucinates in class. Meanwhile, he, Moretti, and a RCMP officer track a serial killer who is stalking Pierce's former therapist. In the end both he and Moretti faces life altering decisions.