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Idea I've had for a bit:
Jirachi game
xxx years ago
Hoenn, larger and different shoreline, different geographic features. Ex, the volcano is dormant and snowcapped and the desert is larger and more open, reaching the shore and without raised cliffs on its borders
You live on mossdeep Island, during low tide its easier to cross to the mainland
Traveling to the mainland is dangerous because the island is home to the regi clan and the draconic tribe who are warring, both are hostile to outsiders
You find jirachi and spend the game nursing it back to health, earning the right to make a wish when the time comes. Eventually it becomes a team member.
New traversal mechanics like rope and vine swinging, balancing. All overworld traversal mechanics (except things like flight obviously) have a limited unassisted version where the trainer climbs, swims etc on their own, and an assisted version that is basically just what happens in PLA.
Regi clan boss wants to use Regis to fight rayquaza, because he wants to revive kyogre and groudon but knows Fug will be there to stop him. Draconic tribe obviously wants to stop this.
Regidraco and eleki added under meteor cave and where abandoned new mauville will eventually go, respectively
At climax, Regi clan boss kidnaps jirachi, uses a mcguffin to force it to give him a wish, wishes for control over rayquaza, allowing him to use the orbs to bring back kyogre and groudon without concern, hoenn gets wrecked
Rescue jirachi after traveling through parts of a now ravenged hoenn, ultimately use the wish to free Fug from the regi bosses control and ending the cataclysm.
At the end, we see hoenn recovering and how the cataclysm changed its geography into the hoenn we see in gen 3, and we see new settlements on the mainland as well as former regi clan and draconic tribe members that fled hoenn during the cataclysm have settled sootopolis and others have started connecting their boats together in the south.