I have been discussing here for some time as a guest (Red Carpet) an I have posted a now obsolete theory for Oscar Ardiles under the pseudonym Red Blood Cell.After believing it could be Gale Bertram I finally have come to the conclusion that Red John is Sheriff McAllister.
Let me summarise all the clues and hints I find important. I will give well-deserved kudos to the posters who noticed something before me.
1. McAllister matches the description of Rosalind Harker well enough, which is "just under six feet tall, with short, straight hair, not muscular but not soft, with strong hands“. He is balding now but he might have had more hair when he visited her 5 years ago.
2. He is the right age. According to the script McAllister was supposed to be 45 years old in 2008. In S05 E13 it’s been established by Patrick Jane using the statement of Father Peter Dibuono, that Red John must have been under 30 when drawing the smiley on the barn in 1988. McAllister was 25 years old.
3. There is a striking similarity between the restaurant owners in S01 E02 and the Carter’s in S04 E01. On the outside both couples lead a respectable, normal life but have a secret murderous „hobby“ in which both spouses take enthusiastic part in. The Carter’s have been disciples of Red John and so might have been Boatwright’s.From what we know of Red John’s ideas he rejects the moral codes established by society. He encourages his disciples to act out their darkest desires.
4. In S01 E02 he acted suspiciously during the interrogation of drug dealer Hector Ramirez. Hector only starts talking after what seems to be confirming eye contact with McAllister. It seems like McAllister is directing him.
5. Also in S01 E02 McAllister seems to try to frame Hector for the murder from the beginning to protect his protégés: „My bet is it’s a meth head from the city coming in off the interstate.“ (Kudos to IKnowWhoRedJohnIs who posted this as a reply to #5008.)
6. In S01 E02 he exhibits a strange forceful behaviour towards Van Pelt by trying to get her into his car. He did’nt meet her and Rigsby before and he didn’t know about the trap laid out by Jane so he probably didn’t know she was part of Lisbon’s team.
7. In S03 E04 Red John’s mole O’Laughlin flies Van Pelt for lunch to Napa. McAllister is the Sheriff there.
8. In S02 E23 Red John comes to Jane’s rescue wearing pointed toe boots. McAllister is wearing similar boots in S06 E03. He refused to climb the ladder because of his pointed boots: „You want me to climb all the way up there in these pointed toe boots?“ (Kudos to shoespeople, who did catch that in #5964 - I also uploaded screenshots there.)
9. According to Sophie Miller’s recordings about J.Roth „there is every indication that his phobia issues are real whether acrophobia or some other issue“. He claimed to have acrophobia, but it could very well be another kind of phobia.In S06 E02 Lisbon wonders why Red John hadn’t killed her and Patrick answers „Maybe something spooked him and he couldn't go through his usual routine.“When Lisbon searched the abandoned house she opened a door to a room with pigeons. Some might have gotten out and scared Red John while they where shut away during the murder of Partridge.Also in S06 E03 on the spire McAllister got scared by by a pigeon and did shout „Hey, hey! Get it out, get it out!“ before he regained his posture and smoothed over the awkward moment with "Didn't see that coming."(Kudos to GaetanoCastobello for guessing this kind of phobia before anyone else in #5302)
10. Red John seems to have an exceptional sense of smell. Remember S03 E23?: „Your wife was very clean. She smelled like coal tar soap and lavender. Your daughter smelled like sweat and strawberries and cream. I suspect it was some kind of kids' shampoo.“Not only could he smell and identify all those things he also remembered every detail.In S06 E03 MacAllister could smell organo on a body that’s been laying in water for some hours. (Kudos to JayJayLaRoth who mentioned it first in #5963)
11. When McAllister shot Charlie on the roof he joked about it: „Now he's talking directly to Jesus!“. He’s someone who kills easily, who doesn’t care about the death of others and makes fun of religious beliefs. (Kudos to JayJayLaRoth who mentioned it first in #5963)
These are enough clues for me to strongly believe Red John is McAllister.He has been on the show from the second episode where he could observe Jane and where he got outmanoeuvred by Jane. I suspect his strong obsession with Patrick started at this episode.