If you watch Fire and Brimstone, the very last shot you see in the house, BEFORE the explosion is  Jane facing the 3 suspects with the tattoo, as they're lining up against the wall. 

Someone shouts "No don't!"

And I think I know who. I found an old picture, which is a shot of Jane's house taken after the footage inside the house cuts off. You can tell this is later than the footage, because in the episode, McAllister is still doing up his buttons again at the wall. But in this picture his buttons are now done and his hands are up. 

http://images.latinopost.com/data/images/full/991/the-mentalist.jpg?w=600


I can only guess Jane turns round to point the gun at Haffner, and Haffner shouts "No don't!"



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In episode 6, Jane says Red John would never not admit to being Red John. In Jane's house, McAllister says "You got it wrong. I'm not Red John".
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For what it's worth, in all of season 6, Jane's not said he killed McAllister. Even Fischer admitted in the trial that Jane never specifically said he killed him. She said it was implied. 
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You can't write an episode called "Red John" and not have him in it. Jane compares pigeons to tiny dinosaurs at the start of the episode. The very last shot of the episode, "Red John" is standing at a dinosaur slide with his hands behind his back. The music is creepy. That's cryptic enough so that 99.9999% of the audience will miss it, but the observant fan will spot it.