Hello, I've been lurking here for months and have been so impressed with the many fascinating interpretations people have come up with. I decided to register so I could mention a theory I developed after rereading The Autobiography of Dale Cooper as no one has mentioned it anywhere that I have seen:
imo Twin Peaks is an allegory for human existence. The doppelgangers are the darkness within every living being, and when we succumb to negativity we tap into an infinite reservoir of evil which we can bring forth into our waking reality. After rereading Cooper's book, I noticed that there are numerous suspicious murders of people who are associated with Dale, and BOB clearly visits him and his mother in their dreams. Dale has no memory of any of the murders - sounds familiar...
I believe that Mr C literally is Dale Cooper, as much as Season 1 & 2 Dale Cooper is Dale Cooper. Hence why he asked Diane "Do you remember everything?"... He does... If the book is implying what I think it's implying, Cooper has been committing murder and sexual assault since he was a child, starting with his neighbour Marie.
At the end of this arc, he becomes whole again, and this means recognising and accepting his actions as both Cooper and Mr C. He is both of them again, and this completely unnerved Diane as she recognises that the man who assaulted her is literally the Dale she loved. Cooper is struggling to deal with his actions and is trying to make things better but fails and Judy is still creating absolute havoc for him and Laura, throwing curveballs at him via the Chalfont family.
Another thing from the book.... Did anyone else notice that Cooper's casual sex partner Andy's father is a fireman and she left him to move to Holland?
I think you're onto something here, but I don't think that the versions of Cooper are all in the same dimension or timeline. My "theory" is that they are all one soul, and Evil Coop is the darkest degradation of the Cooper soul while Agent Cooper is the brightest and best of the good.
In episode 18, I think we see something more toward the center.
I am interested that your brought up this autobiography (which I haven't read and I haven't seen discussed much if at all, although maybe it has been).
When Cooper was in the junction room with Naido the exit that went to Doppelcoop was numbered 15. After the switch was thrown the room changed to one that came out near Dougie Jones and was numbered 3. My thought is that when Cooper used the Great Northern key numbered 315 it was like he came out of both exits, or united the differents aspects of the different versions of Dale Cooper.
Anecdotal evidence for this is exhibited entirely within the final two episodes. First, Doppelcoop, when he shows up at the sheriff's department is offered coffee and refuses it. Soon after, the real Cooper calls Frank Truman and tells him to get the coffee on, demonstrating that the exuberance that he has for coffee is very much intact. Finally, in the diner in Odessa the waitress asks if he wants coffee and he merely nods indifferently. This is basically exactly between the attitudes of Cooper and his doppelganger.
My thoughts on why this might be are that all three Coopers involved had been erased from existence. The doppel and the tulpa had both vanished, as did Laura. So I believe that Dale intentionally went to where erased things go to try and retrieve Laura Palmer from the dustbin and when he stepped through the door he merged with the other versions of himself that were previously deleted.
Let's let Kyle MacLachlan answer this:
http://variety.com/2017/tv/news/twin-peaks-kyle-maclachlan-finale-1202547022/
Did you feel that Richard, in the finale, was a distinct character of his own, or just Cooper with a different name?
He was… different. The way it was described to me, he’s just a little harder. So it was another variation, sort of a subtle variation obviously, compared to the other two, but a subtle variation of Cooper. And so that was that last hour, Watching him navigate that.
Lynch doesn't tell his actors what their character's motivation is, he tells them what they need to know to portray what he sees in his mind. I think the possibility remains.