Dining with Diane

So the Dale Cooper in our world is a doppelgänger possessed by Bob, while the real Cooper was trapped in the Black Lodge

Evil Cooper goes on with possessing people and making them murder, torture, mutilate, just like Killer Bob did 25 years ago

The Real Cooper can now finally leave the Black Lodge, but to do that he has to replace Evil Cooper, trapping him in the Black Lodge (?)

Evil Cooper created another doppelgänger, Dougie, so that when the Real Cooper tried to leave the Black Lodge, he would replace Dougie and not Evil Cooper

Now that both Coopers are in the same dimension, Evil Cooper seems to have lost some of his abilities and makes a less-convincing-Cooper (the FBI agents are not sure he’s the real Cooper)

It’s also known that both of them can’t live in the same world, so one of them has to die now

Things that still need to be explained:

The glass box seems to be some kind of man-made portal to other dimensions (seeing as the Real Cooper had to go through it to come back), but who built it? Why were they watching it, waiting for something to happen? Whoever built it, knew that Cooper was going to come back? If so, did they want to help him or prevent him from coming back?

What is that “spirit” that came from the glass box and mutilated the 2 people?

Something that still hasn’t been explained: who is Bob? He’s an evil spirit, yes, but was he someone that was possessed too long ago? Or is Bob his human shape?

My evil doppelganger was behind the glass box as an early warning system in case I ever found my way out of the Black Lodge.  He did not expect Bob’s mother to show up first and kill his staff.  

That is listed as “The Experiment” in the credits.  It is the creature summoned by nuclear tests, and Bob hatched from an egg it laid in that region.  

Bob was explained in episode 8.  He is the winged toad that crawled into the mouth of a young lady I suspect was Leland Palmer’s mother, and from there began possessing various victims to further harm the world.  He is the personification of the evil that men do.