Before you down-vote me just because of who I accused, hear me out.  

Immediately from the opening scene of S6:E7 we are hit with an improbable scenario.  While three suspects are burnt to an unrecognizable crisp, two suspects and Jane are alive, intact, with not a scratch or burn on them.  Their clothes weren't even singed.  How is that possible?  

Theory 12346 (http://www.whoisredjohn.com/See-a-theory-Red-John/12346) gives an interesting explanation as to why Jane, Bertram, and Smith were not harmed at all.  I disagree with this theory, though, that it was Stiles who brought the bomb.  I believe it was Bertram.  Right before Bertram stands up to line up against the wall, watch his left foot.  He's shuffling something underneath the sofas!  Why would he do that?  Well, didn't this last episode give you enough reason for why he'd kill in cold blood?

I don't think, however, that Bertram is Red John.  I think he's high up among Red John's cronies, but not the big guy himself.  According to the interviews with Bruno Heller (if we can trust anything that he says), the final showdown takes place in a park, at the request of Simon Baker.  In the previews, we see someone--with the classic strange voice used to portray Red John throughout the series--enter the church.  Jane shoots this individual.  I can think of a few explanation for this.  What I want to happen is this:

Bertram enters the church using a voice distorter, showing Patrick that any person could sound like Red John.  Jane kills Bertram because Bertram threatens his life--he obviously has weapons.  But, Bertram isn't Red John.  Jane later kills Red John when Bertram reveals a final clue to him.

It's odd, as Theory 12346 also points out, that Jane went public, calling on the media to get the news out.  It's clear to me and the writer of Theory 12346 that Jane is taunting Red John the same way he taunted him the first time.