Ok, in 06x03, Patrick noted that the sheriff was afraid of birds.
In 06x08, the shit episode, Patrick said he was disappointed that he was not expecting the red john were Sheriff Thomas McAllistar.
So, if was not expected, why he brought the pidgey to scare "Red John"?
In my opinion , he knew that were 2 explosions, he knew that sheriff was alive and brought the pidgey, but, if he knew that Bret Partridge faked DNA infos, he could do the same thing for Haffner and Stiles, and , in 06x06 Jane looked at McAllistar's eyes when he says "I'm not Red John" . C'moon Patrick can see when  everyone is lying, why he didnt shoot in that time?


Sorry for my bad english, and i hope Red John's story has not done yet!