Woo. Go watch the episode Red John again. When talking with gale Bertram Bertram says I hate to tell you but km just a humble foot soldier for the BA. BRETT John is the top brass. He said Brett not red john. A very subtle hint. Plus if McAllister was red john he wouldn't need to kill Bertram as a loose end because he was planning on showing himself regardless to kill Jane. If he needed Bertram dead he would've let him and Reede die in the explosion and just faked his own death then disappear. It was when Bertram hinted Brett john to Jane that sealed the deal for him. It couldn't get out that Brett partridge is red john. Plus Jane was testing McAllister when he asked him if Brett partridge helped him fake his death, weeks after partridges "death". Add in the obvious that partridge would need to know how to fake a death to help McAllister and you've got very subtle hints that partrdige is still alive. If the BA contacts people while remaining unknown then partridge wouldn't need to die since he wouldn't know the person calling or why they he was planning. If McAllister was red john he wouldn't need to kill partridge or Bertram is what I'm saying. Plus McAllister never said he was red john. He said " I am the Blake Association " meaning he was sent there by the top guy, Brett partridge to kill Jane and Bertram, who is suspected of being red john, so the real red john can escape and live freely.

My guess. Partridge is red john and helped McAllister get the body and DNA the day McAllister found out where they were meeting, after partridge fake his own death, so McAllister could survive and wouldn't be killed. McAllister helped partridge get the body to fake partridges death as well. If you look the body has long hair in the back and partridge had cut his hair short so it can't be his body. In return for helping McAllister live partridge asked McAllister to do him a favor. Save Bertram and smith and make Jane believe one is red john. Then kill them both to make it look like they killed each other in a duel to the death. That way McAllister could live and partridge, red john, could also get Jane off his back because he was getting too close. It all wpukdve worked too if jane wouldn't have suspected McAllister and brought the pigeon.