Okay just for the sake of proving that no matter how terrible Heller messes up the story line, it can still be fixed even though it's extremely unlikely.  And to prove that no matter how delusional my past theories have seemed, I can still get more delusional just for the fun of it.  Remember how Strawberries and Cream had a part one and two?  The Red John episode is also two parts.  We've seen part one where nothing makes sense.  It all comes down to what happened in that house before it blew up.   Jane has Reed, Bertram, and McAllister against the wall.  McAllister breaks and starts confessing about the tiger tiger organization, that's when the "no!" we hear before the gunshot happens, Bertram yells to get McAllister to stop and Jane fires a warning shot that stops all the commotion.  McAllister tells Jane about the tiger tiger group and makes a deal with Jane to help him in exchange for immunity.  Jane knocks Bertram and Reede Smith out.  He lets Stiles and Haffner go in exchange for their promise to lay low until everything is over.  Haffner is reluctant but Stiles agrees and promises that Haffner will do as he's told.  They drive away in the car that passes Lisbon.  Jane and McAllister go get three bodies that Jane stole from the morgue and put them in the house.  Jane also broke switched the DNA in the computer.  They drag Bertram and Reede into the next room and Jane makes McAllister promise to meet in the church in two days.  McAllister leaves and Jane blows up the house with himself, Reed, and Bertram in the room over just before Lisbon gets there.

From Jane's preparation it is easy to tell that he knows that RJ was never one of the people on the list.  The list was a list of tiger tiger suspects given to Jane by RJ to expose the tiger tiger club as I explained in my previous theory:  http://www.whoisredjohn.com/See-a-theory-Red-John/11369.  Now, how to explain the episode we just watched as Jane's elaborate con to catch RJ.  First,  Lisbon's phone was bugged by RJ in the first episode of this season.  That was the major clue, RJ called Jane on Lisbon's phone.  Second, where is Lisbon's phone?  Jane stole it from her when he hugged her before abandoning her on the side of the road.  Jane doesn't take the phone with him into the house before he blows it up so the first RJ hears about the bomb is from the media and perhaps from local police.  RJ assumes that the tiger tiger club set the bomb to kill the tiger tiger suspects and Jane before the organization was revealed.  

Jane announces to the press that Bertram is RJ and the manhunt begins.  At the end of Fire and Brimstone, Jane goes to the church where he agreed to meat with McAllister.  Jane lays out the plan to catch Bertram and RJ.  McAllister is able to contact Bertram using secret tiger tiger methods without letting Bertram know that he's still alive.  He instructs Bertram to kill off Jane and suggests that Bertram pretend to be RJ to lure Jane in.  McAllister and Jane finish planning and split paths.  Jane goes back to his loft and recovers Lisbon's phone from where ever he put it so we know that RJ is listening again.  All Jane has to do then is wait for Bertram's call.

Moving on the the church scene.  Jane and Bertram have that little talk and then Oscar shoots Bertram.  Now, Oscar knows McAllister so when McAllister steps into the church, Oscar follows McAllister's instructions and waits outside.  Jane still has Lisbon's phone with him so RJ hears the entire pretend conversation between Jane and McAllister.  RJ thinks that McAllister is the head of tiger tiger and is pretending to be RJ.  RJ hears Jane defeat McAllister with a pigeon and then shoot him, shoot Oscar, and start on the chase.  But the gun was a prop, so McAllister wasn't actually hurt which explains why he was able to run a mile.  RJ hears Jane chase McAllister down, the 911 call, Jane's disinterest in explanations, the psychic claim, the sound of strangling and death, and Jane's call to Lisbon that it's over.  Then Jane throws the phone away meaning that RJ no longer has ears on the situation.  

RJ is going to be furious.  It is going to tick him off that Jane thinks he's some bumbling idiot that got defeated by pigeons and was a coward that called 911.  The beginning of the next episode will start from RJ's perspective.  RJ will meet up with Jane and they'll start talking.  Jane will explain everything that I just explained in just a few quick flashbacks that makes everything clear.  RJ will explain tiger tiger's presence in the season 3 finale which will explain why RJ sent Jane a list of tiger tiger suspects.  
Jumping over to Lisbon's perspective.  Based on what Abbot(?) tells her about the church crime scene, Lisbon is going to realize that Jane has a con going on and that he faked McAllister's death.  She'll then go looking for him to save him from the real RJ.  Alternatively, she realizes Jane is about to go into hiding and she'll never see him again so she goes looking for him.  Lisbon gets the team to help her escape from the FBI and she goes to find Jane.  Jane never expected Lisbon to be able to find him and it is a great indicator of how well Lisbon has come to know Jane that she succeeds.  She walks into where ever it is that Jane and RJ are and is surprised to see that Jane is not really making escape plans.  He's just sitting there talking to Walter Mashburn of all people.  "Hi Jane, Hi Walter"  This puts Jane into a very awkward position because he just realizes that he encouraged Lisbon to sleep with RJ and he desperately wants to protect Lisbon from the knowledge that she slept with a serial killer.  Walter's just standing there smirking because he thinks the whole thing is very funny.  Jane is also is the position of admitting to Lisbon that he's been lying to her since the season 5 finale.  Jane tries to get Lisbon to go and his concern has her realizing that Jane thinks Mashburn is RJ.  She's the one that mentions the elephant in the room and starts trying to convince Jane that Mashburn can't be RJ because she slept with him and . . . and . . . and . . .she punches Mashburn square in the face.   Mashburn uses this opportunity to escape and he goes off and kills Rigsby and Van Pelt because we know they're not returning for the rest of the season.  There has to be loss on both sides for RJ's death to seem real.  What would the ending of Harry Potter have been like if none of the good character died to balance out Voldemort's death?  Now either Mashburn escapes and Jane tracks him down two years later in South America where he kills him or Jane kills Mashburn and then flees to South America because he could never prove that RJ was Walter Mashburn.

Actually, after writing this theory out, I can see it happening next week.  If you watch the promo for next week, it looks like the Mentalist is changing into a soap opera so that may just be another red herring.  And when everyone hears about the huge reveal next week, they'll all come back.  Anyway, no matter how it turns out, I've had fun on the website so let's say our goodbyes in the comments below unless of course my last and most delusional theory turns out to be correct and then I suppose I'll see you all next week.