So whatever happened to Agent Dale Cooper?

Answer 1

I always wondered about that too. David Lynch obviously had something in mind for the next season when he showed Agent Cooper replaced by his evil doppleganger in the season finale, but the movie "Fire Walk With Me" was a prequel, not a sequel, so we may never know what would have happened next.

However, there was a strong hint in the movie, when Annie said, "The good Dale is in the Lodge, and he can't leave. Write it in your diary." So he was trapped in the Black Lodge and if there had been another season it probably would have dealt with his efforts to escape.