>>34888113Gen VII was going in the right direction with a more personal plot revolving around Lillies family. Make something like that but with the protagonist's family and you have a good basis.
You could have something like the protagonist's father wishing to use the box legend to bring his dead wife back to life but doing so would harm many others. Since it's a Pokémon game it would all resolve with you letting go and learning to deal with loss.