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What about agriculture and industry? Pull a Ruby/Sapphire deal where there's two diametrically opposed "teams" of villains.
Agriculture
>Grass/Ground
>Based on a prehistoric giant sloth with moss growing in its fur. Dex entries say that it keeps the seeds of every known plant in its moss, and spreads them around the planet by travelling to desolated areas. Originally an ally to humans, it grew disillusioned as humans began to industrialize and pollute the environment. In a rage, it destroyed a massive factory before disappearing. No one has seen it since...if you have this version of the game, the main villains are a team of radical environmentalists in opposition to a conglomerate of reckless industrialists.
Industry
>Poison/Steel
>Looks like Exploud and Heatran fucked and the kid was raised by Muk. A mechanized mess of smog-spewing smokestacks, powered by an internal furnace. Originally a sludge-like pokemon similar to Grimer, it absorbed early human machinery into its form and became a powerful new creature, capable of smelting, welding, and providing power on an industrial scale. The discovery of this pokemon was instrumental in the industrialization of the pokemon world, but the waste it produced was why the Agriculture pokemon attempted to fight back. The Agriculture pokemon destroyed the factory where it worked, burying it under the rubble. It's lain in the abandoned, derelict factory ever since, waiting to be reawakened...if you have this version of the game, the villains are the industry union, who are trying to smash the environmentalists that are working against their factories.