Sheriff Thomas "Tom" McAllister was the sheriff of Napa County and the serial killer known as Red John.
He first appeared in the episode Red Hair and Silver Tape, when a girl was murdered and he helped the team to investigate.
Patrick Jane and CBI agents Teresa Lisbon and Kimball Cho arrive at a vineyard where a female body has been found and are met at the scene by Sheriff Thomas McAllister. Patrick and McAllister watch as Teresa and Cho examine the body. They find a stab wound that doesn't appear fatal, no signs of ligature marks, and that the victim's gums are livid and eyes hemorrhaged. They believe she's been suffocated. Patrick informs them that the girl was a local, and her death was an accident. He explains that the killer didn't intend for her to die that way. Since the victim was still clothed, Patrick speculates that the killer was taking her somewhere to sexually assault her. She made too much noise at the wrong moment, the killer tried to keep her quiet and smothered her by mistake. After that, she was no good to the killer, so the body was dumped in a place only a local would know. McAllister asks Teresa about Patrick and is told that he was a consultant with the California Bureau of Investigation. McAllister asks Patrick if he's clairvoyant or psychic and Patrick replies that he has no powers but pretended to have them once. A slightly confused McAllister asks him what he actually does for the CBI and Patrick invites him to play a game of rock, paper, scissors. Patrick proceeds to beat McAllister six times in a row. McAllister is baffled and somewhat frustrated that Patrick easily selected the winning choice each time.
Back at the sheriff's department, Teresa and Patrick question Hector about his relationship with Melanie. He tells them that he was supposed to meet Melanie at the restaurant at 11:30 pm but showed up 10 minutes late and thought she hadn't come out yet. He waited a few minutes then drove off because he was impatient and got upset. Patrick feels that Hector is telling the truth. Teresa thinks Hector did it and points to a timeline drawn on a chalkboard illustrating that there wasn't enough time for anyone else to have entered the parking lot, abducted Melanie and driven away. Patrick stares at the timeline for a moment and agrees that there wasn't enough time. He notices Frankie O'Keefe looking around and waiting in the sheriff's department lobby. Patrick takes him to a diner for a snack and asks to see the gun hidden in Frankie's backpack. Frankie replies that he didn't have a gun. Patrick calls rookie CBI agent Grace Van Pelt and tells her that Teresa has changed her mind about the motels and that she should check on them and call him back with any information. After he gets off the phone, he asks Frankie if he was going to kill Hector with a knife. Frankie opens the backpack and shows him a hatchet. Patrick tells Frankie the story of how he lost his wife and daughter and tries to explain that the hatchet is not the best solution. He then receives a call from Van Pelt about the motels.
Jane sets a trap for the killer, wanting to create an opportunity. Van Pelt and Rigsby are at the restaurant. They pretend to have an argument in front of the entire restaurant, and Rigsby storms off leaving Van Pelt by herself. She leaves the restaurant and begins walking alone on the side of the road. She runs into McAllister who tells her it's not safe and offers to give her a ride. When Van Pelt refuses, he becomes insistent that she go with him and Rigsby races over from the surveillance van and knocks McAllister to the ground.
Sheriff McAllister returned in the second episode of the sixth season, Black-Winged Redbird. In the third episode, Wedding in Red, Jane travels to Napa Valley to investigate Sheriff McAllister. McAllister saves Jane's life from the killer. He's not scared of high places, like the church's deck, but he hates pigeons, he hunts wild animals and has pointed toe boots like Red John.
In Fire and Brimstone, Jane tries to gather all of the remaining Red John suspects in one place, which included McAllister. Here it is revealed that he, along with Gale Bertram, and Reede Smith, all share the "three-dot" tattoo that Kira Tinsley mentioned to Jane, which later turns out to be a mark of the Blake Association.
He's declared dead in the explosion of the bomb in The Great Red Dragon, but was discovered that he was alive and survived the bomb blast (thanks to the body with fake DNA provide by Association member Brett Partridge).
After Jane uses a pigeon to scare McAllister and kills Oscar Cordero, the wounded McAllister runs away from him. After a lengthy foot chase, McAllister tumbles to the ground and attempts to phone the police. Jane then kicks the phone out of McAllister's reach. Jane asks McAllister if he is sorry for killing his wife and child, to which McAllister replies "yes", and then proceeds to ask him if he is afraid to die, again McAllister responds with a "yes". Jane then slowly chokes him to death.
In the end, Red John turned out to be Thomas McAllister, the bumbling sheriff who seemed to be the least likely candidate for the serial killer. This is precisely the theme the show wished to portray, that Red John was not a perfect man who saw-all, knew-all, did-all. He was simply "the man next-door". Most of the time, this is the case in true life serial killer scenarios, as well.