I want my theory to be the real one, and in my mind this would be it.
Here is my theory if you are interested.
Kirkland is indeed killed by Reede Smith.Michael (Bob's twin brother),
finds out that the Blake association is behind his beloved brother's
death.This upsets him, in the point that he rebels against the
association and Red John of course.
Michael (with the help of
Visualize and Bret Stiles) managed to get sober, built a remarkable and
unique personality. He is evil, no doubt, because he is the right hand
of a serial killer.He gets angry learning about how and why his brother
died, and he starts feeling guilty, because he realizes his mistakes.So,
he approaches Jane, he tells him everything about the
organization and the tattoo.He also tells Jane the name of Red
John.(improvise here). For me that would be Partridge but whatever you
like just put him in his position.Now, Jane knows who Red John is, but
still he needs a master plan to make him reveal himself.He
invites all the remaining suspects in his house.Partridge must act fast
in order to keep his secret safe.Unfortunately for him, it's too
late.No one dies in the explosion.Red John has a lot of
links so he can easily dumb dead bodies with DNA evidence on them
suggesting that the suspects are dead.The two alive ones (Bertram and
Smith) remained alive so the game will continue.Stiles and Haffner are
with RJ's part of course, because the Blake association and Visualize
are helping each other with their goals, so one is obligated to help the
other.Jane's reaction is immediate.He knows there is
no way that Smith is RJ, especially after his confession.The guy passing
by the interrogation room is Michael.Then Jane goes
and reveals Bertram as RJ.The whole attention turns to Bertram.He runs
away because if he doesn't he will possibly die by RJ or someone in the
association.RJ is getting furious watching his whole work to be credited
in Bertram, so he leaves a message that only Patrick could decode.It
says that he is RJ and he wants to meet with him, both without any guns
or backups.Jane agrees.Bertram appears in the church telling to Jane he
is RJ.Of course he doesn't believe him.Then the real RJ walks into the
church and kills Bertram while saying "An other thing I can't stand is
when someone gets credits for my unique work."And then he appears
wearing his classic cape and mask.On his side he has
Lorelei,(she is not dead, there are enough clues to prove it:
http://www.whoisredjohn.com/See-a-theory-Red-John/13493 .Lorelei was
trying to kill RJ, when he figured it out, he persuade her that he
didn't kill her sister and take her on his side again.Together they make
the video,sometime after Jane finished the list)
Jane stares at him
while he is extremely tense.(Like the season 2 finale). Neither RJ nor
Lorelei are pointing him with their guns.PJ stays stunned, while the two
walk all along the hall.All of a sudden, Michael makes his appearance
this time at the side of Patrick.Red John says: 'Michael, I feel
betrayed and impressed at the same time.Well done"
Michael answers 'You really shouldn't kill my brother"
while hearing these words starts to think about her sister again, and
freezes.Jane seems so surprised for all the things that are happening at
the same time.While RJ is some steps ahead of Lorelei, she is pointing
him with her gun.RJ turns around and kill her.Then PJ gets the moment to
take off his weapon.He manages to shoot RJ but not so bad that he
manages to run away.Jane and Michael start to chase RJ.But when they
arrive at the park there is a little surprise for them.They find
themselves surrounded by people all wearing the same capes and masks as
RJ does.Patrick loses sight over RJ because he becomes one with the
crowd.Then they all start: 'Tyger, Tyger burning bright, in the forests
of the night.What immortal hand or eye could frame thy fearful
Then they ask Patrick and Michael to throw their guns.They
do it of course.Right after, RJ's voice saying "Step aside'.The crowd
separates and RJ appears.
"You are a clever man Patrick, you just
never used your intelligence appropriately.I'm smarter than you,
obviously.But you could achieve so much more if you were by my side"
Patrick: 'You take pleasure from killing people, that's not clever, that's paranoia'
RJ: "So you say'
Patrick: 'So I say.I'm gonna kill you, and God is my witness.'
RJ: 'Look around you.The game is over and I won'
Michael starts to run, distracting the crowd while Jane chases RJ.He is
wounded, so he can't run.Jane takes off a hidden knife and backstabs
RJ, while the FBI/CBI arrive at the scene.PJ takes off RJ's mask and
beneath, it's Partridge.He starts saying things about Jane's wife and
daughter such as how they were dressed, how they smelled, that Jane's
daughter was indeed sleeping and never was scared, that Jane's wife
fought for her life and that she was the most difficult victim to bring
down.Then he starts telling details about the way he was cutting them
open.Patrick cries while listening all these, and strangles Partridge
while he is ironically laughing.RJ finally dies and it immediately
starts to rain.Jane gets on his knees, he cries and smiles at the same
time, looking to the sky with his hands in the air.
Hope you enjoy.