In the season-three finale, "Strawberries and Cream (Part 2)", Jane encounters a man (Timothy Carter, played by Bradley Whitford) in a shopping mall who convinces him he is Red John and whom he subsequently kills.

In the season 6 episode "Red John", the eponymous serial killer's identity is revealed to be Thomas McAllister, the sheriff of Napa County, portrayed by Xander Berkeley.

In the season 2 episode "The Scarlet Letter", Jane tells Senior Special Agent Sam Bosco (Terry Kinney) that "Red John doesn't make mistakes.

Bruno Heller, show's creator, has said that Red John isn't a "pathetic loser who is hiding out in a basement somewhere", and that Jane is "not fighting the Green River Killer.

Jane soon realizes that Red John is more powerful than he could ever imagine, having connections in law enforcement and an entire cult of brainwashed followers under his complete control and at his beck and call.

In the second-season finale, "Red Sky in the Morning", a man claiming to be Red John appears in the flesh, wearing a black sweatshirt, apron and pants, black rubber gloves, a pair of charcoal boots, and a grotesque rubber mask that covers his face, making him look slightly similar to what many believe the real life serial killer Jack the Ripper donned during his murder hunts.

He ultimately suspects Supervising Agent Madeleine Hightower (Aunjanue Ellis), due to DNA evidence that Jane believes has been planted by Red John or one of his accomplices.

When Lisbon does so, a phone rings near Jane and is answered by a man (Timothy Carter, played by Bradley Whitford) reading a newspaper and speaking in an odd, high-pitched voice.

"[6] In the season 4 premiere it is revealed that Ron Deutsch, the bald security officer at the mall, was a Red John operative who removed crucial evidence from the scene.

Jane comes to believe the man he shot was not Red John, but Timothy Carter, a sadistic businessman who, with his equally twisted wife, Sally, had kidnapped a young woman, Debbie Lupin, in whose search the couple cynically pretended to join.

A couple of hours after the television appearance, Panzer is found murdered, with Red John's smiley face painted in blood on one of the walls near his body.

At this time, Red John is shown to be stalking Darcy via an uploaded video called "I Dare You" on the Major Crime server, which shows her in her apartment, unaware that she is being filmed.

Darcy interviews Rosalind Harker, Red John's blind ex-girlfriend and also the attendant of the morgue that Timothy Carter's body was taken to following his death.

Jane, fearing Red John will kill Harker, alerts Lisbon and Darcy, and they proceed to her house with an FBI SWAT team.

In season 4's finale "The Crimson Hat", after being fired from the CBI, Jane finds himself in a Las Vegas bar, where he meets an attractive woman named Lorelei (Emmanuelle Chriqui).

Darcy opens the back door, which reveals CBI Director Luther Wainwright, bound and dead, with a pay-as-you-go (burner) phone attached to his body.

Lisbon faxes him a photo of the crime scene where the word "ROY" can be seen scrawled on the floor next to the sister's body – information that had been withheld from the public at the time of the murder.

Lorelei reappears in episode 16 of season 5, "There Will Be Blood", which reveals two new accomplices of Red John – well-regarded citizens Julia Howard and Jason Lennon – an employee and a trustee of a women's shelter, respectively.

Two weeks later, Lennon is revealed to have survived the shooting, although in a coma, while Lorelei is found dead under Red John's smiley face with Homeland Security and police at the scene.

The leader of the cult, Bret Stiles, has shown in previous seasons that he has a very thorough grasp on Red John's inner workings, hinting at a connection between the two, which seems to finally be revealed as Visualize.

In the episode "Red Letter Day", Kirkland has two Homeland Security agents break into the attic where Jane works (and occasionally lives) at CBI.

Jane had suspicions that he was being watched and realizes that his room has been broken into because he sees the toothpick he had been leaving of late between the door and the frame lying on the floor where it fell after Kirkland's men entered the premises, never noticing it.

In the premiere of season 6, Jane is highly disturbed at how Red John could deduce who he would have on his final list two months before finishing it, as well as have so much intimate knowledge of his memories and thought process.

After repeated attempts to communicate with Sophie fail, Jane visits her house, only to find her severed head in the kitchen oven, revealing her to be one of Red John's victims.

However, Red John didn't know that Sophie used an audio device to record her thoughts about her patients, using her unique ability to read people even if they attempt to hide their true emotions and personality.

Locating an entry dedicated to a man with the last name "Roth" (a word meaning 'red'), Red John's alias when visiting Sophie, Jane listens to a detailed description of Red John's inner workings; he seems to have a case of acrophobia, and/or other phobias, is middle aged, is in good health, has no family but many friends, is a great speaker, has good posture, is an excellent whistler, possesses hints of narcissism, and seems to be harboring something dark within himself.

Jane moves in to take a closer look at whom he now believes is the real Red John before Bret Stiles indicates for him to look at Gale Bertram and Reede Smith, who both have the same tattoo as the sheriff.

This prompts Jane to reveal at a press conference that Red John is Gale Bertram, who has since gone on the run with the aid of a fellow Blake associate named Oscar.

While hiding from the authorities, Bertram brutally murders a bartender who comes close to recognizing him on the news reports and evades capture by posing as a SWAT officer as other units, many of which he called in himself, arrive, allowing him to escape unseen in Oscar's vehicle.

With this secret organization at his disposal, in conjunction with the dozens of loyal followers he recruited, seduced, and brainwashed through Visualize, McAllister formed connections all over the state to spy for him, tamper with evidence, commit murders, and aid in his plans of building up his society and cult, as well as targeting Jane and people close to him.