Something really big that would get attention, I think, is to have something stir up all or most of the restless spirits. This could cause both the massive hauntings and bring attention to Kanto. The main "graveyard" in Gen II was in Kanto, so if the source of the hauntings is there, it would make sense characters would go over to stop it. Especially if it spread to Johto and nothing would stop it unless the spirits were settled at the source, almost like plugging a leak.

Maybe bring in a Legend, too, to get more than just "we need to fix this" types involved; D/P flavor text mentions that Giratina appears in an old cemetary, so it wouldn't be much of a stretch for it to appear in Lavender Town, I don't think. It might be too big and cast off from the main idea, though, so that's just a thought.