What if Mr C is Cooper corrupted by being trapped in the time loop searching for Judy? Every time he passes through the loop he loses part of himself. Mr C is the tragic end - a man reduced to base instinct and the sole drive of finding Judy, even using BOB's help to achieve the goal.
The Coop we meet at the end - Richard Coop - is his first step on the mission to find Judy. Bad Coop is the end.
I wonder this because 'Good' Coop ends the show with the same goal Bad Coop seemed to have.
I don't think it's that simple.
Remember Judy wanted C to go away so Bob could be sent back to the Lodge.
C seemed aware that Judy wanted him back there since he had "loopholes" prepared.
As for the last Cooper, one visual element I think is powerful is this :
When they depart, it's broad day light, and they arrive at night.
It's a transition from Light to Dark, and I feel it's exactly what Cooper went through.
Basically, I think mister C was a malevolent and shadow created from Dale Cooper, while the Cooper at the end is a darker Cooper.
Think of it as a spectrum, positive neutral negative.
Mr C isn't just a "negative Cooper", as he has his own motivations and will.
The ending Cooper is a negative Cooper, same motivations, same character, just on the "other side" of the spectrum.
Which happens to mimic some of C's mannerism because he was also a negative being, despite being another person entirely.
That's how I see it anyway, because Mr C never quite felt like Dale Cooper, evil or not.
