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My idea that will never get made is to have a corporation fill the role of the villainous team. A bit like Team Rocket, but with no cheesy "Team" in the name. Its fighters are made up of employees. It also hires gangs of several sorts to act on its behalf in a mercenary capacity to hide its true intentions. The story revolves around economics and energy in some way. The corporation wants to dominate the region not because they're "evil", and not because of some "prophecy". None of that shit. Their antagonism comes from their methods and results. I want to include Pokemarts somehow but I don't know how to connect them. Maybe the corp owns all the Marts and is trying to force their way into the energy business to vertically integrate their supply chain. Something like that. The CEO is the final boss, and the Directors are the sub-bosses. Maybe a gym leader is secretly also the leader of a gang.
The region features a few different power stations. One coal-fired, one hydro-electric dam, one nuclear plant, a field of wind turbines. The corp, through their hired thugs either tries to sabotage or take over the plants. They overwork the Pokemon in the coal mines, they force the electric pokemon to generate power unsafely. I don't know whether to have the mons die in these situations or not. And though it's not terribly original, they of course also steal pokemon.
The role of the professor is taken instead by a group of rangers or maybe breeders, perhaps your parents are part of this group. A professor is met later in the game.
The starting town is high up in the mountains, but not quite high enough for ice pokemon. A river flows down through the mountains, and the first few settlements follow it to the coast. The first major city is a port on the first landmass, a ship takes you across the strait to the second landmass. All new region of course. General aesthetic similar to Johto with some Kanto and Sinnoh mixed in.
Using the hg-engine with overworld wild mons.