I've been reading these forums for a while and I agree with the collective here that the final reveal was disappointing. Mainly due to the fact that none of the questions were answered and none of the clues throughout the five seasons turned out to be relevant.
In light of this I think we should do our own endings. In my scenario Ray Haffner would be Red John and it would be him with the 3 dot tattoo and the fear of pigeons instead of McAllister. This is my script for the church scene, everything else in the episode I'd keep the same:
HAFFNER: You didn't know me you don't know me. You have no idea.
JANE: I know you're an orphan, I know your parents abandoned you. I know that made you grow up with a feeling of abandonment, which is why you crave commitment so much.
HAFFNER: I don't crave commitment, people just give it to me on a plate.
JANE: You don't crave commitment? Isn't that why you made all the members of your precious Blake Association get a tattoo. A permanent, incriminating tattoo. If the secret ever got out it would be easy to incriminate the entire society and everything you built would come crashing down. Not very logical is it?
HAFFNER: Look at Gale over there. As you can see I tie up loose ends pretty well.
JANE: Are you tying up loose ends, or preventing a further feeling of abandonment?
HAFFNER: Oh easy there Freud! Like you said the mark is incriminating. I have to tie up loose ends and sometimes cut off loose shoulders.
JANE: The mark, that's what you call it? That's what Renfrew was trying to write. Renfrew didn't actually know your real name but he knew you were marked with the tattoo. He was writing "HE IS MARKED"
HAFFNER: You know I actually came back to the scene of my crime, I could have taken that off but I thought it would be funny to have that confuse you. What theories did your bungling detectives come out with? He is many? He is married? He is many times smarter than I am? You still don't know how I fooled you do you? How did I survive that bomb?
JANE: The bomb gag is simple. The first was a concussion grenade, knocked everyone out...
(flashback shows Haffner running away and throwing the grenade)
... The second lethal bomb that killed McAllister and Stiles only after you dragged Bertram, Smith and Me out of harms way.
HAFFNER: Correct
JANE: Faking your own death was easy. Brett Partridge was Blake Association. His job gave him access to the primary DNA database. He switched your DNA records with a body that you had on ice, a surrogate, and you brought the body to my house in the trunk of your car and you put it alongside Stiles and McAllister.
HAFFNER: Very good, your hindsight is 20/20.
JANE: You even killed Stiles, he was like a father to you!
HAFFNER: A father? Are you kidding me? I'll admit there was a time when I respected Bret. He could make anyone do anything. I once saw him gain someone's lifetime commitment using just kinds words and a flower. Taught me a lot about the law of reciprocity. You give a little, and gain a lot in return.
JANE: A trick you used all your life. Maybe you should be thanking him instead of blowing him into pieces.
HAFFNER: It wasn't a big loss. My respect for him diminished when I learned over time that he actually believed all the crap he was spewing. He was just a loon.
JANE: A loon? Coming from someone that's been killing women for 25 years?
HAFFNER: They shouldn't have said the things they said about me. Their men should learn to keep their mouths shut.
JANE: And that warrants killing people does it?
HAFFNER: Deep down you understand. We're not that different you know Patrick. Lorelei is right. You should have accepted my hand of friendship when I offered it.
JANE: You mean WAS, and Lorelei WAS wrong. I'm nothing like you.
HAFFNER: I mean is, Lorelei is still alive. Faking a death is easy when you got disciples in forensics. The CD was filmed after you whittled down the names and left the pictures in your apartment ripe for anyone to break in and take a peek. You didn't actually think I was psychic did you? No it was all part of the game. I was just planting the seeds of doubt into your mind. And I must say it was fun.
JANE: I've been planting seeds of my own.
HAFFNER: Oh yeah?
JANE: Yes, in fact just a few hours ago a planted bird seeds all round this church.
(Patrick throws bird seeds on Haffner, put his hands to his mouth and makes a loud pigeon call. Masses of pigeons from outside the church descend onto Haffner. Haffner shakes in a panic, drops the gun and falls to the floor. Patrick picks up the gun)
