This is my theory on how things happened in Jane's house:
1. First we heard a gunshot: The only one that had access to a gun was Patrick; Besides, if somebody had in fact a gun the only possible target would have been Patrick Jane, and none of them would have failed that shot (as they are all police), so, who Jane shot? and more importantly why?. 

Haffner tried to make a move, Patrick sees him and somebody yells "wait! no", well that's Stiles trying to stop patrick to shoot him, Patrick shoots and Stiles takes the shot for Haffner. So, now we have a dead guy, 3 suspects, and Haffner who is now furious; at the end of the day Stiles is his leader and mentor. Jane finds out in a situation where he lost control; he won't be able to figure out who RJ is, but luckily he has a plan B, he hided a bomb in his house, so he detonated it. And the rest is history.

Talking a little bit about the bomb, there is no reason why RJ would have to detonate a bomb, let me explain: if Haffner (or Stiles) is RJ he is not gonna be interrogated, and if he is any of the others three Patrick will not be able to figure out which one.

Moreover, both Bob and Brett are dead, there is no reason too put such a creppy weirdo as a charismatic mastermind, and Bob was declared dead by tyger tyger.