You need to think like an actual screenwriter/designer in these situations, since you can do anything to your own property in Amurrica (and Europe and most of other places if you live there). You be creative, and it's going to be fine, trust me. Just end the game after the most intense part has passed for a couple of minutes, and you'll be fine (as to not leave cliffhangers). It's called "pacing".
Also, something to note is that the cinematics engine of Pokémon IS actually the game itself (and vice-versa if you wish) There are many ways to end these stories, the least being an example from BW.
PS Watch the internet show "Extra Credits", and you'll find lots of good ways to start and end thine wonderful hacke.