First of all, I think now, like most of us, that Bad Coop isn't Bob but doppelganger but there are still some points that I like about my first theory ( written by myself in other threads).

If we assume that Bad Coop is in fact Bob then who we do see in the end of Part 4? Maybe it's not Bad Coop pretending to be someone else, but "our" good special agent Dale Cooper... Of course damaged, neurologically impaired but he' s back. Just like Leland actually, he's got official explanation for his actions and he believes it not having memory of his evil acts.

Let's remember that Bad Coop tricked Lodge ' s rules by creating and sending Dougie there so he avoided coming back, but in fact he thrown out evil from his gut by vomiting. 

Now because of situation being out of balance, we've got two Cooper ' s bodies with one divided soul. What is missing from agent Cooper is all what poor Dougie has. Definetely one of them has to die... And Bob flown out somewhere, probably back to Twin Peaks where he belongs.

Does that theory make any sense?

And I'm sorry for my poor English...