Well, if anything, it looks like Black Hat has never persisted in long terms, with what we've seen in some pics from his mansion and how Earth hasn't fallen into damnation yet, so I'm guessing for the finale it's either
a) Black Hat cannot exist in the same host for a long time and either has to return to the hat or is forced back into it.
b) Somehow Flugg's incompetence or 505 will end up destroying BH for good (not really likely)
c) BH is sent to another multiverse.
d) The original body will find a way back to control its body or some shit and both BH and the OG host will die?
e) something edgier happens.>>107934659
He even sang the original pokemon song in one part of the movie.