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We've had "rule the world" (Rocket), "shape the world for one set of adaptations" (Aqua & Magma), "shape the world for nothingness/'the greater good'" (Galactic) and "help free Pokemon from oppressors/take over the world" (Plasma).
Religious cult with zealots that banish Pokemon for being mysterious creatures, thus they're obviously demonic. The Professor goes against the law and grants you a Pokemon, but is later caught and arrested. You make your way through the region to rally support for the proper education on Pokemon, while battling in underground gyms. At the climax of the game, the cult "damns" a Pokemon they declare "evil" for being dark type. This Pokemon is thrown into a pit, only for you to rescue it. Because of your allegiance to the Pokemon, you're taken as being evil yourself, and face the leader of the cult, who summons a deity of light (which is lol, a Pokemon), and battles against you and the Pokemon of "darkness".
Plot holes galore, and obviously needs a lot of filler and editing, but oh well. Basically if Ghetsis was religious, and Plasma was his religion?