Original Theory. None of That Suspect Crap. None of that Patrick Jane is the main character crap. I will finally tell you who Red John really is.

Red John is the Joker:

Wayne Rigsby is Batman, and Bret Stiles is Alfred, his faithful butler. That's why Bret Stiles doesn't have a house in his own name and all his assets belong to Visualize- Batman has been using it to fund his exploits for years. Bret Stiles for the past months has been hiding in the batcave under Visualize buildings as Rigsby realizes he must protect the ones he loves as he gets ever closer to capturing the Joker.

Van Pelt is the Joker's daughter, and the Joker has been using her to get closer to him. But Wayne has caught on to this and is using this against her, to track the Joker down. In a move of genius, he marries her letting her finally think he will spill his secrets. Van Pelt tries to draw Stiles away to the Joker, but does not succeed. Rigsby finally has enough information to track down the Joker.

The woman feeding pigeons is Red John aka the Joker. Look at the long hair, the weird make up on her face. The smile he draws represents how the Joker had his mouth cut, and the smile is ironic, as the Joker's smile is a permanent blood red scar to his face.

Patrick Jane manages to invite Alfred into his house. This was the Joker's chance. He could kill Alfred. The Joker rides to Patrick's house on a massive red dragon, and its dragonfire devours the house. As it is a dragon it can breathe its flames with pinpoint accuracy; it only made sure Stiles was targetted by the flames. However since Haffner is always there kissing Stiles' ass, he was also killed.

 On the day of reckoning, in the park, Batman assaults the Joker in a frenzied tazer attack. Usual Batman Vs Joker Rules dictate neither may kill the other one. "Why won't my directors ever let me kill you?!" says Rigsby. 2 Tigers jump out of nowhere. Batman beats them down with brute strength. Jane follows Rigsby, and realises Red John is there. They're both writhing on the floor, drooling from the intensity of the tazer shocks. Patrick sees his chance and chokes Red John to death.

When Batman realises his favourite enemy is dead, he vows vengeance. Patrick has to flee to Mexico. Batman retreats into the shadows...waiting...watching.