Gale Bertram, the mastermind, is Red John.
Below are 2 links to my old theories. Please read them first.
http://www.whoisredjohn.com/See-a-theory-Red-John/1849
http://www.whoisredjohn.com/See-a-theory-Red-John/3183
Now, Timothy Carter told Jane "When O'laughlin told me about your trap..."
How did RJ know it was a trap? It could be just real. Bertram knew about the trap, because Lisbon told him a different room number. The moment O'laughlin told him about it, he knew. Bertram arranged Timothy act and he left just after Jane started to talk about killing Todd Johnson. It is a very important topic, about a mole in CBI, and Bertram simply leaves the scene, nonsense.
We know for a fact that Kirkland is not after Red John. If he were after RJ, he would ask Jason Lennon who RJ is. Instead, he killed Jason. Although he seems like they were after RJ, they were actually after Lorelei. Nothing can persuade me that Kirkland is hunting RJ just like Jane. If he were, he would ask. If he cared about knowing who RJ is, he would move Jason to a secure floor and question him. It was obvious that Jane would visit again, he knew, and he did not care. He had no intention of learning RJ's identity, he was there to kill Jason so that Jason does not speak. It was about damage control.
Why were they after Lorelei? Because Lorelei became unpredictable after her relationship with Jane. She needed to be killed.
Why did Kirkland order his team to collect info from Jane's room? Because Bertram wanted to know how close Jane is. Kirkland studied everything just like Jane, and came up with the list.
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So, we know that Kirkland is with RJ. Yet, how to know if he is RJ, or some else is RJ? Simple.
The second link above explains the whole season 3 finale. We can clearly understand that season 3 finale was very well planned. It was meant to be that way. So, Bertram's role is critical, irreplacable by enything else. Bertram is in this too.
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At this point, one can say, both of them can be disciples of RJ. Could be right, but unlikely. These guys are very high profile. Involving someone else could mean blown covers.
Remember season 3 finale? When Jane told Bertram about making deal with Hightower, he hasitated for a second, then said OK, and just after Jane left, he picked his desk phone and pushed a button. I used to think, he is calling RJ. But no, he was calling Timothy or Kirkland to see if they could arrange a surprise party for Jane.
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Kirkland is Bertram's right hand.
Kirkland kills Rebecca in CBI building. He collected Jane's RJ data for Bertram so that Bertram can come up with a list.
Remember the talk in Bertram's office with Kirkland after Lisbon leaves?
Kirkland: Can we trust her?
Bertram: Can we trust anyone?
Two murder buddies talking about whether they can trust Lisbon and Patrick to catch Lorelei.
Does this dialogue ring any bells?
When Jane was talking to the father from visualise farm, the father told Jane about a 50 year old guy calling the painter of smiley face "kid". Father had talked to the man in farm about the face.
Father: What does it mean?
The Man: What does anything mean?
Maybe little Bertram and the old man were like Dexter and his father. The old man guided him, showed Bertram the path. Now, Bertram is mentor of Kirkland, just like he himself was once.
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In the end, before the end of this year, we will know that Bertram is RJ.
Bret would never help Jane about freeing Lorelei from prison. He would not sign his death contract.
Sheriff and Reede Smith, i won't even bother considering them.
Brett Partridge called Jane "jerk" behind him, not possible.
Ray Haffner, nope. Bret Stiles would know.
Take Bertram and Kirkland out of the RJ equation, and everything collapses. If you take Bertram out, you can't explain season 3 finale, and if you take Kirkland out, you can't explain killing Jason without questioning him and chasing Lorelei so badly.
Season 3 finale is the key, and we shall see. Bertram is Red John, and Kirkland is his right hand.