Patrick Jane's alter ego is Red John.
This is something I have suspected for a few seasons now. The primary reason I suspect it is because it is still a possibility. To this point in the series no one has seen Red John. We thought the tattoo was an indicator of Red John himself however in the most recent episode we find out that it is actually a mark that many have, and it is the mark of the minions of red john. So in a sense there are literally hundreds of red johns because all of the members of the Blake association take their orders from some unknown figure, i.e. Red John. This only leaves one loophole for the Jane as Red John theory. Lorelei Martins. The audience is led to believe that Lorelei let slip to Jane that she wonders why Jane and Red John had not become friends when the shook hands but this is misleading and I believe Patrick Jane misinterpreted this comment. I don't believe Lorelei Martins has ever knowingly met Red John. That makes her far to much of a liability, Most especially when almost every other Red John associate knows very little about who is directing them. To openly reveal himself to Lorelei as Red John to her would be most anti Red John behavior. I believe that the person whos identity is unknown to Lorelei but who she believes is Red John has intimated to her that he knows Patrick Jane very well. Well enough to have shaken his hand. Which would be fitting if Red John is infact Patrick Jane. I believe that was the mistake, for the Red John to intimate how well he knew Patrick Jane. If youve read this far I thank you and now I will bring it full circle. I believe that Patrick Jane is schizophrenic, or a savant of some kind that enables him to be the clairvoyant character we see each episode but I also believe it his (for lack of a better term) "condition" gives him the power of Red John. Every step of the way Patrick Jane has been the smartest person in the room which makes him the number one candidate to be Red John if he is already known to the audience. Now there are significant questions to be answered, number one being Why would Jane kill his own wife and daughter? that is an answer I do not have however I believe that it was not the intention of Jane to do so. I dont even believe he did it with his own hands. If i was guessing I would say that the murder of Jane's family was a miscommunicated order to one of his minions or if Jane did it himself an act symbolizing the embrace of Red John within himself. I believe the murder of Jane's family psycologically shook Jane into the CBA consultant we see. But I believe it is also what blocks Jane from realizing he is Red John. And finally, In the last episode, the great red dragon we see Jane's Mug shatter. Jane's reaction is not one of sadness or depression, it is one of revelation. I think when his Mug breaks it is a psycological jog of his memory from some other stressful point in his life (my guess is the point that created Red John). In the final scene of The Great Red Dragon episode we see Jane in a church. It is my guess that he is starting to uncover that he is Red John. -