It looks like Kirkland, Bertram, McAllister, and Smith have formed a brotherhood which is involved in dirty covert operations. They're after Red John just like Jane is. Somehow they see Red John as a potential threat to their operation and they're planning to get rid of him. On the other hand they don't want him to get caught by the good cops, since he might know enough to put them down, I'm guessing Red John has even threatened them already. That's why Kirkland broke into Jane's room to get the list of suspects, and that's how Bertram knew Jane was getting close.
Did you notice Bertram's face when he learned Partridge was dead? He was genuinely surprised and kind of shocked. Maybe Partridge was part of the brotherhood too or somehow connected to it, which is the reason why Red John killed him. The only piece of data that might belie my theory is the fact that Kirkland didn't ask Lennon about Red John's identity, which would suggest he already knew him, then it wouldn't make sense for him to follow Jane's progress on the Red John case unless he is Red John himself or an accomplice, which would totally blot out my theory. I think I've been looking at it the wrong way all along, with the presumption that Kirkland knew what we knew namely Lennon being Red John's accomplice. Jane and Lorelei were the only ones that knew it back then. So what if Kirkland killed a potential Red John witness for an entirely different reason without having the slightest idea what he was actually doing?
The conversation Bertram and Kirkland had plus Homeland's access to the Red John case, and the conversation Smith and Bertram had after Jane left all support my theory. I believe Red John will kill one of the them very soon.
