Theories on how it ends?
The scenes with ??????? at the beginning are the end, note the FBI pin missing from Dale. He is dressed as Dougie was in the last few scenes.
It is in our house now I believe Dale leads Bob or it into the white lodge and it is prisoned there with him. He locks himself away in the white lodge to keep it away from this plane of existence.
The question is what it is and is Richard's behavior a sign that it is loose around Twin Peaks right now. I really think Dale traps Bob in the White Lodge but in the process can never come back to this plane.
As I've said before in another thread, I wonder if the Good and Evil Coopers are actually two sides of the real whole Cooper. So, rather than seeing one defeat the other, they may actually combine to form the whole person.
It might not happen like this, but it would make sense to me if it did (in as much as Twin Peaks can make sense). I just find the whole Good versus Evil thing a bit too childishly simplistic in a comic book superhero kind of way. Real humans are a mixture of good and bad. Nobody is 100% good or 100% bad. Even the nicest person you've ever met will occasionally have a bad day or a bad moment where they cut someone up in traffic or scream at their partner out of frustration.
Cooper surely must have had his bad points and some darkness in him. When he met his doppelganger at the end of Season 2, maybe that was like a mirror being held up to show him his dark side. If he had been a perfectly good person, he would not have had a dark side to be shown to him.
Another possibility is that the Good Dale might no longer exist, so we may never see the old Cooper we loved. Remember in Season 2 when Hawk said that in the Black Lodge you will meet your own shadow self, and if you meet it with imperfect courage it will utterly annihilate your soul.
Or maybe it really will turn into a comic book style farce and the two Coopers will rise up into the sky and shoot each other with lasers until the Evil Cooper is finally killed by the Good Cooper and then there are no more bad things in the world and we will all live happily ever after and walk off into the sunset.