Pokemon Tabletop United campaign

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I'm fishing for ideas for a Pokemon tabletop game that I want to run for some friends. They plan on running a sudo legit criminal organization to the tune of the poke-Illuminati. So far it looks like two players are interested in empire building, two players are looking for a more tradition Pokemon adventure, one guy wants to explore everything and the other guy is going to be a ghost assassin.

I have a good idea on how I want to main overarching plot to shake out, what with another criminal team already being a thing and contesting them at every move up to the climax where the leader ends up being a god Regigigas masquerading as a pokemon researcher and trying to turn humans into Pokemon in order to exert control over them. But really that's something that comes up at the end and I'd really appreciate some ideas for some short-mid range plot arcs to give them something to do. Thanks in advance