At the end of The Great Red Dragon, Jane walks into a church . . . WHY?  Jane doesn't believe in God and the only other time he was in a church was when he revealed his fake breakdown to Lisbon . . . that's a hint!  Jane's in a church again and we're about to learn about whatever con he's been playing.  Plus, that elevator scene was just like the elevator scene in S4 finale where Jane leaves to fake his breakdown in Vegas.  Nothing is as it seems . . . Jane would never go to the church to seek heavenly help so he's there to meet someone and it's not Lisbon like last time!  It's RJ and who else do we see in that church?  A women on the left that looks like Lorelei and a guy on the right that looks like Mashburn.  Mashburn has a really distinctive hair cut plus it looks like that guy is wearing a red turtleneck and we've only seen Mashburn wearing red turtlenecks.  Also Jane was very on edge walking into that church because he knew he was about to meet with RJ

RJ IS WALTER MASHBURN AND WE SAW HIM IN THAT CHURCH AS JANE WALKED IN!

I'll post a picture in the comments.

At first I was dissapointed about the great Stiles dying in such an unhonorable way, but after thinking about it for a while I concluded he may have sacrifised himself. 

Let's overlook what might have happened in the landhouse: Jane lines up the three Tigers, ready for a long interrogation/execution. Meanwhile Haffner is using Jane's focus on them at his advantage and tries to escape because one of the Tigers might know he's the real Red John. If he is, he has been there before and knows a way out of the house by the back.

Jane has a fast reflex, turns around and shoots him. He hit him, but not lethal, maybe he shooted off a finger or something (DNA 'evidence' after the cleanup).

Jane goes after him. Bertram goes after Jane to disarm and kill him (in the spirit of the Tigers). So they both are found in de next room after the explosion. Smith is reaching for his gun on the ground.

Meanwhile McAllister sees that Stiles is picking up a bomb (that might have been hidden in his shoe, what would explain the bare foot). He tries to stop him but it's too late, the bomb goes off and Stiles & McAllister are blown up. Smith was just far enough to survive, as were Jane and Bertram, who were struggling for the shotgun.

Stiles was the one that went to the army for a small but effective explosive. He knew Haffner, a lifetime protegee of him, very well, and probably knew he was Red John. Since he was allready a dying man, he debated the events with Haffner in advance and told him to run if possible, and that he would do the rest (or Haffner asked him the other way around). So there's DNA from three men, while only two are dead. 

Jane knows Haffner is Red John since he tried to escape (Haffner was allready eager to leave before the gunshot) but uses the 'fact' that he deceased in his advantage and sets up Bertram as the perfect distraction. By declaring on TV that Bertram is the serial killer named Red John, he's ending things as they begun: by offending Red John publicly. Jane knows he's too proud not to come after him now.

Not a theory, but still interesting. There's this Mentalist fanatic on Youtube; his name is Americ and he's part of a channel called HappyCool. He makes wonderful weekly reviews of The Mentalist, and he occasionally gets the privilege to see episodes prior to airtime. 

This is Americ's reaction to the Red John (Season 6 Episode 8) episode. There are no spoilers, only Americ's reactions coupled with some soothing music.

Definitely worth the watch, and if you can let me know what Americ reacts to at 1:38, I would love to know. Is it an RJ reveal, or is it a Jane-Lisbon moment?

Link: http://www.youtube.com/watch?v=vWYpReqi678&feature=c4-overview&list=UUamPGTREfS0YRJBkC7cBHPg 

Enjoy and continue theorizing. I love them.