I may have a similar problem. I've got a fantasy story that resolves around my MC becoming bitter, twisted and a menace. I can't do that in any believable way without three stages.
1st stage is some bad things have to happen to a likeable character
2nd is justifiable acts of revenge
3rd is the anger taking over and him not caring who he hurts to get to the people who've wronged him, and extending his anger to anyone who tries to defend them.
Far too many words for one book, and a story that falls into three parts rather than two. So I figure each stage is one book. It means I have to end my first book with there still being people around who haven't faced justice, and I need to leave my MC in the company of a character who the reader knows is a bad influence, but who is acting to help my MC.
To do this I needed more characters. Some to face justice as a resolution, some to survive. The characters who provide the immediate danger and conflict in the book have to have resolved storylines at the end....even though I like them and wanted them to stick around.
I've decided that part one ends when the characters reach safety after a lot of threat. it doesn't end their development but it ends the threat and conflict of part one. The safety has to be reached by dealing with the immediate threat though, not just hiding from it.
By the end of the book my MC should still be likeable but he'll have done some bad things and be under the influence of a bad person. hopefully the reader will forgive him as he's done bad things to people i'm painting as bad, even if they're really a shade of gray.
If I'm lucky enough to be sell it and the only three people to buy it then no-one should miss part two but they will wonder a little about the fate of the bad influence. I can't resolve his story in part one without blowing parts 2 and 3 out of the water. I think I can justify that by using the principle that " the enemy of my enemy is my friend, even if he's an utter ####" deal....so at the end he's an ally who has secrets.
I also took things out of part one I wanted in. I'm keeping a couple of factions who will clash apart as I don't want that unresolved in part one and I can't resolve it until part 3, so it got cut.
I suppose my rambling point is that to end a story, I think your character has to be good enough for your reader to forgive them any bad behaviour, or there needs to be some kind of justice for the bad things they've done, otherwise the loose ends might be too loose.
Craig