Still a few things I can't explain, but here's my theory. Patrick is Red John, but he doesn't know he is. Gradually over the next few series, Lisbon will start to work this out. The entire thing ending with Patrick himself coming to realise that he is indeed the man he has hunted all along. Patrick will have no choice but to kill himself in order to kill Red John. Lisbon will want to stop him, to save Patrick. Lisbon will fail, Partrick will commit suicide. Split personality basically. Like Jekyl and Hyde.