With serial killer Red John laid to rest, Patrick Jane is finally free to close the door on his past and plan for the future. A fresh start with the FBI has him solving top-security cases alongside former CBI agents Teresa Lisbon and Kimball Cho, new colleagues Jason Wylie and Michelle Vega, and boss Agent Dennis Abbott. And Jane's blossoming connection with Lisbon brings a deeper bond to the partners' already intimate and intense professional relationship. But when femme fatale Erica Flynn resurfaces from Jane's past and another sadistic serial killer appears on the scene, affairs of the heart take a backseat to survival.
Jane and Lisbon begin their new relationship, but they must hide their feelings for each other from their colleagues as they investigate the murder of an undercover agent. Also, young, ambitious agent Michelle Vega joins the team.
Lisbon goes undercover as a prison inmate in order to get a convict to turn on her boyfriend, who is the leader of a high-end car theft ring.
Jane and Lisbon travel to Beirut where they must work with Jane's familiar adversary Erica Flynn, who agrees to help the FBI apprehend her boyfriend, a courier for terrorist organizations, in exchange for amnesty for her past crimes.
The team investigates a murder linked to a counterfeit diamond operation, but an illness forces Jane to direct his colleagues from the office as he recuperates. Meanwhile, Abbott is concerned that transgressions in his past could harm his wife’s chance to obtain a prestigious job in Washington, D.C.
A chance encounter with a military colonel leads Jane to believe the soldier is hiding something, leading him to dig into closed murder case of the man’s wife.
The team is brought in to consult on a botched DEA raid, but when Abbott’s former boss tries to blackmail him into keeping the agency’s missteps quiet, Abbott is forced to choose between his career and his morals.
A murder investigation becomes personal for Lisbon when she learns that her underachieving younger brother, Jimmy, is being sought as a key witness.
Jane worries for Lisbon’s safety when the team puts itself in the line of fire to protect the witness in a murder investigation from a skilled assassin.
When Abbott’s old boss, Agent Peterson, threatens Abbott’s career – and possibly his freedom – Jane devises a risky plan to protect his friend’s future.
Jane takes extreme measures as the team tries to apprehend a deadly gang of armored car robbers before their desperation to remain free costs more innocent people their lives.
A young man claiming to have psychic powers offers his help to the FBI in solving a pair of murders, but when he leads them to additional victims, Jane and the team begin to suspect that he is in fact the killer they’re hunting.
Jane agrees to once again pretend to be a renowned psychic and be used as bait in an attempt to lure out a serial killer and give the FBI a chance to apprehend him.