This Theory covers the Red Moon episode mostly, but also has more things in general. Also, I prove that Brett Partridge is not Red John (in the end of theory). But before that, my humble opinions about the series:
I started to hate coming up with theories. The reason is that for almost every single character in the series, we can come up with a solid theory, and it can be true when RJ's identity is revealed. I read somewhere that Bruno said that a good observer can find Red John. Well, we observer everyone and find that everyone can be Red John. To make sure that we would never be %100 confident about who RJ is, they added so many fake clues that it started to be disgusting. Now, everyone is a possible RJ, and everyone is a possible friend of RJ.
Turning to analysis
Let me start with general information. Patrick Jane has never ever been a step ahead of Red John during the series. Only when he was acting down for 6 months, but Red John learned Rigsby was not dead and he was ahead again.
Red John knows that Patrick solves cases by setting traps for suspects.
If we assume that Ellis Mars is Red John
In this episode, Ellis Mars patiently waits for the person in charge. He wouldn't talk to Van Pelt, waits for Lisbon. But actually he was waiting for Patrick Jane, because he knew Lisbon wouldn't be interested in his psychic crap and he would be able to speak to PJ.
He says: The killer is to strike again.
The killer does.
Later Mars tells Lisbon that she was the last person to speak to murdered sheriff Mullay.
Also correct.
How can he know these? He has to know that killer is Todd, and he must also have been talking to him. Mars was not the actor of the play, so he can be the director or scriptwriter.
In the hotel room, Todd can't kill Mars. He is in trap, and he tries to shoot PJ with the gun. When pulling the trigger, he says The big picture would blow your mind. He fails, is taken into custody he wants to talk to Jane, saying that They have something in common.
And when he is dying in hospital room, he says: Tyger Tyger
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Now, as I said, Patrick Jane was never ahead of Red John. Everything went according to RJ's plan.
In the hotel room, Todd doesn't kill Mars. Why? I will explain in a second. But before that, he tries to kill PJ. Why did he pull the trigger? Because he knew the gun wouldn't fire. They would never kill Jane. RJ knows that PJ always uses traps to catch suspects, and he knows that PJ would never use a gun that works. It is loaded because Todd would be able to distinguish the weight between a loaded and unloaded gun, or he might wanna check the bullets. So, there is no firing pin. He draws his knife, and PJ calls Cho and Rigsby.
When Cho and Rigsby come, there is a smile on Todd's face. Everything is going according to plan.
Now, why didn't he kill Mars? Since this episode is a work of Red John, everything must be arranged before. If there was no Ellis Mars, there would be no trap. So, Mars is an essential part of the plan. Mars is not a random guy. There is no way he would know those things.
Either:
1) Mars is Red John's friend, who is playing his part in the game.
2) Mars himself is Red John.
Todd knew he wouldn't be able to kill Mars even if he pulled the trigger, as he knows gun won't fire. His part there was to be caught in trap. He acted like he couldn't shoot.
But, someone sets him on fire in CBI ( probably by Craig O'Laughlin, though never evidenced as far as I know ). Now, when he opens his eyes in hospital, he says, tyger tyger. What the hell?
If you are betrayed, and tried to kill by a horrible thing like being set on fire, the first thing you would say is the name of Red John. But instead, he says tyger tyger. This can only mean one thing. He knew that would happen.
So what crazy mind accepts being set on fire and killed? Answer is all actors of Red John. Rebecca was smiling when she was killed. The assassin going to hotel room to kill Hightower died gladly by jumping. The guy keeping the girl in the house also died without telling anything. This could be a thing about the higher path Red John was talking about in season 4 finale.
I strongly believe that the episode Red Moon was for Todd. He played his part for the higher path and died. It was Red John's gift to Todd.
Another thing about this episode, Todd says, the big picture would blow Patrick Jane's mind. He is not saying that identity of RJ would blow his mind, but the big picture. So, RJ can still be a side actor, but not Ellis Mars. The thing to blow Patrick's mind would be the game played in this episode.
Lastly, the building used in last episode of season 2 where Jane and RJ met is the same as the building for sheriff in this episode.
http://i46.tinypic.com/w02r2p.jpg
http://i45.tinypic.com/w9a88o.jpg
Interesting? Yes. This could be a hint to us, or maybe they ran out of buildings.
Now, as promised, I will stop talking about Red Moon and prove that Brett Partridge is not Red John.
How do I know? In season 2 finale, you remember the fake Red Johns killing some girl. The couple in film club at college. At that episode, PJ goes to house of the murdered girl and starts looking around. Brett Partridge is also there. He is saying things like hurry up we real guys should find actual evidence. Patrick Jane says some things to him, irrelevant to my proof, and goes out of the room.
When Patrick is out of room, Brett says: JERK ( Season 2 Finale, Time: 11:06)
This is the proof that he is not Red John. He is just an amused scientist. Why? Because when he says JERK, there is no one in the room, only Brett. Nobody can hear him. And Red John would never call Jane jerk. Red John likes playing games with Patrick, and he possibly admires his success in cases. A smile, it would be what RJ would do, but calling him jerk? Never.
