Before I begin, I should state that I've watched every episode up to episode 6 (Fire and Brimstone). 

I know that lot of people are thinking that Brett Partridge is still alive and that he is Red John. I did have a thought though. In all the best horror movies, unless you actually see the dead body then they're not really dead. Even though Partridge is reported as being dead, we never actually see a dead body. Could he still be alive? Read on.

In a previous theory I wrote, I stated that Tiger Tiger group (TT) is a separate thing from Red John (RJ). What I mean by this is, RJ may be aware of TT and what they do, but is not actually a member. 

Given his number of contacts and influence, RJ could definitely have come into contact with TT members, even if he himself wasn't a member or even in law enforcement. However, I think that RJ must at least have been in law enforcement at one point in order to learn the best ways to leave no evidence at his crime scenes. During this time, maybe TT tapped him up to become a member. But instead, he could have easily persuaded them to help his cause as Red John. He charmed them (in the way a charismatic enigmatic person like RJ could) to help cover up evidence at his murder scenes and maybe even becoming one of his disciples.

I think that Brett Partridge was part of TT. TT has figured out that RJ is using some of it's members to cover up his crimes and is trying to find RJ to weed out those in the organisation who are helping him. They used Partridge as bait, but RJ being one step ahead, called in the anonymous tip that went to Lisbon. That screwed up TT's plans to catch RJ. However they faked Partridge's death and have him locked up in a dungeon somewhere possibly torturing him for info on RJ's identity.

This would explain why Partridge said Tiger Tiger to Lisbon. He felt betrayed and wanted to expose the organisation. Also, if TT have Partridge captive and tortured him for RJ's identity, it would explain the abundance of swat team members outside the house in the promo for the episode The Great Red Dragon, currently available on youtube. They want RJ as much as jane does and are determined not to let him get away.

In addition, Sophie Miller (Jane's ex-therapist) stated on her dictophone the following about Jay Roth (ie Red John):

Mr. Roth came in complaining of a recent issue with severe acrophobia. He’s middle-aged, in good health, with no stated prior history of psychiatric issues. He has no living family, but many friends on whom he relies for company and emotional support. He’s well-spoken, good posture, self-possessed. In the waiting room, he sat calmly in one place, needing no distraction.Though I note, he is an excellent whistler. His self-presentation is pleasant, but there are hints in his behavior of a damaged and narcissistic personality. He says he deals with conflict and adversity easily, though. I’m not convinced he’s being truthful about this. In fact, much of what he said, though spoken convincingly, did not match what I can only call my instinctive response to his presence, though I cannot point to identifiable clinical behaviors that indicate this. I sense something deceptive and dark in his emotional makeup. However, there is every indication that his phobia issues are real whether acrophobia or some other issue remains to be seen.

We have seen that Haffner definitely suffers from arachnophobia. There would be no reason to put in a scene like that to highlight a phobia without very good reason. Haffner is ex FBI and CBI agent, so would have definitely have come into contact with TT members, even if he didn't actually become a member.

Haffner is an ex-football player, probably college as seen by the trophy in his office. The trophy is a heisman trophy, as far as I can tell. "Heisman" - He is ma. Coincidence? Could the victim have been trying to write "heisman" but died before he finished it? Or if the message was supposed to be "he is many" (as a lot people suspect) could this be yet anotherreference to Tiger Tiger?

According to Rosalind Harker (who had a relationship with RJ for a few months) Red John is: Just under 6 feet tall. Not muscular but not soft, either. Short straight hair... a gentle voice. Rough, strong hands. This description sums up Haffner quite well (apart from the hands as we can't feel them).

Red John is extremely intelligent, a match for Jane, as seen from his ability to outwit him time and again.   He has twice hacked into the CBI computers without being detected. He sets up phony companies and bank accounts to keep his identity a secret. This would well be within Haffner's abilities; formerly, he was an FBI agent in the Organized Crime Division, and is an expert in wiretaps and creative surveillance techniques.