Okay here is my Farragut theory:
Timothy Farragut is Jason Cooper is Red John. Whenever Stiles tried to kill Timothy Farragut,Farragut faked his death and changed his identity. Farragut then wormed his way back into Visualize to Stiles second in command while Stiles has no clue. Whenever Cooper was humiliated by Stiles whenever Cooper tried to take his place, Cooper didn't later use his alter ego as RJ to kill Stiles because he knew he had to be patient because Stiles was either going to die of cancer or would get his at Jane's house. Once Stiles was dead Cooper would rise to power to be Visualize's next leader.
He would then be the leader of two groups Visualize and his Red John disciples and finally be able to take down the dreaded BA. As someone else on this sight has mentioned when Red John told Patrick:Tyger Tyger
He was trying to give him a hint as to the existence of the BA so Patrick could take it down. Timothy Farragut was not in law enforcement so he was not in the BA and the only thing standing between him and control of California was the BA.
Cooper knew that Jane was getting close when Jane figured out Red John was someone he had shaken hands with so Cooper knew he had to act this time instead of letting Jane act first. I think that one of those guys that Kirkland sent into Jane's office was a member of Visualize and he looked more thoroughly than just at the board. I think that Jane hid his real work somewhere else. That is how Cooper got the list.
Visualize is very good at brainwashing people so I think that Cooper knows a great deal about hypnosis and that is how he made Kristina go brain dead.
I think that the BA sent Kira Tinsley to bug the CBI to try and figure out how much Jane and the team knew about the BA. Bertram doesn't know that much because he does not work with Jane day-to-day and he is tasked with finding out how much Jane knows. ( remember from the meeting)
So Bertram sends Kira Tinsley in to bug the CBI. Jane and Cho figure it out and Bertram or someone else goes to kill her. They made the mistake of letting Kira see the tattoo. That was not Red John that killed her because he would have used a tazer or a gun to kill her and he would definitely not have left her alive.
Jane plants bomb beforehand just in case. When Patrick lines everyone up Haffner goes for his gun. Jane detonates the bomb. Haffner is a Red John disciple and wakes up before everyone else and kidnaps the closest person next to him( McAllister) and takes him to Cooper who in turn hypnotizes McAllister into thinking he is Red John.
•Red John "episode"
Jane kills McAllister and thinks it is finally over. Cooper is glad he got off clean. Takes a break from being Red John and focuses on Visualize. I predict we will hear from Visualize again before the season finale.