The BA was using red john to cover up certain murders .
They did this using macalister and partridge. macalister really was red john in a sense.
The real red john (rigsby) used jane to take down the BA.
I believe patrick. is privy to the whole deal
He faked a breakdown before ;)
Watch how rigsby acts this season. How weird him and van pelt act when the fbi take over . How odd they acted in the car. How conspiring they were in thr room with the usb and cho.
Watch again and tell me what u think.