Bit rough round the edges but I think it fits.
Contains Mild spoilers as well perhaps, and thanks to other theories that had bits that fitted very well.
The whole of the Mentalist saga can pretty much be summed up with the concept of duality.
The Visualize cult is a powerful organisation that has infiltrated everywhere. (promotes religion but is about the money – )
The law enforcement community; frustrated by criminals escaping prosecution through lack of technical evidence created their own unofficial force called the Tiger Tiger Club. This allows criminals to be brought to justice without trial by jury. (thus commenting on the symmetry of behaviour – in and out of law to get the same result) What started out as a way for justice may have mutated into a “monster” fuelled by greed, and its own motives (much like Visualize?)
Both Visualise and Tiger Tiger have been been forced into an uneasy alliance since the events at the barn all those years ago and the continued killings by Red John. Both have infiltrated each others agencies to add to the stalemate that exists (i.e. Ray Hafner – and other suspects) -
Red John was “born” from a then Visualize member who killed in the barn; and has done so to prove a point ever since, empowering himself in his own mind.
Red John is unique as he has the key to the secrets of Visualize and Tiger Tiger, he is a member/has been a member of both, and cannot be easily eliminated as both organisations would risk all their secrets coming into the open. Lower level do not even realize who he is on a day to day level.
Visualise are aware of his previous original identity, but do not know his new name or what he looks like. Tiger Tiger are aware that he is a member of the their own private law enforcement community but are unaware of what he looks like or his name.
Patrick Jane is a necessary evil in this, affected by the killer himself he is being used by both Visualise and Tiger Tiger, to find Red John and eliminate him, however his methods risk revealing the same secrets that Red John could reveal, and this is the irony.
This is what forces all involved to be very weary of the man that is helping them as he has no connection to either organisation. Initially Jane was a suspect in his families murder and targeted by Tiger Tiger, however now he is being used by them at some risk.
Bertram is certainly creepy and head of Tiger Tiger and Bret Stiles is in charge of Visualize. Both cannot stand each other but are trapped in the stale mate, that can be only be solved when Red John is gone.
The real Red John
Indoctrinated into the cult at a relatively young age, was uncontrollable and became a murderer. The reason he has been allowed to last for so long is Visualize hiding his initial murders as their cult was growing.
Visualize gave him a new identity and face which meant that he could disappear and start afresh. He then entered policing as a career and eventually became a Tiger Tiger member. Just guaranteeing a level of movement without any knowing he is Red John.
Who is he?
But he is dead you say?
Well I don’t believe he is, having made a perfect crime scene due to his training and due to assistance from the Tiger Tiger organisation he managed to escape. His official reason for doing this he is concerned Jane or Red John is closing in on Tiger Tiger, after the events of the last series and first episode of this series. (up until he fakes his death)
He was perhaps the mysterious twin that is mentioned, but of course he now has a different face so his old self would have been forgotten. His father and of course therefore Kirkland's father could be Bret Stiles, and that would add another layer to it. Particularity if Mr Stiles is ill due to a disease that needs Bone Marrow or some such. Liver Transplant etc., due to the aforementioned alcoholism that allegedly killed Kirkland's father.
So it is Partridge (Michael Kirkland) and all those involved on the list have somehow played a part in elongating Red john's work.
Hope you like it, sorry if it didn't make sense!!!
Please comment of course as well!