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Rocket. Magma/Aqua. Galactic. Plasma. Flare. The elite four of every region and their champions. So in the games the kid hero takes down these master trainers but more realistically I think that the gangs and the elite going head to head makes more sense. Out of all the teams I'd have to say I love Team rocket best. So after all the worldwide ass whooping and one one-upmanship from both sides, though mostly the elites and champions.
On to the story idea, I'd like for my character, Bailey, the new leader of Team Rocket and pretty much the only one left to go up against either Cynthia of the Sinnoh elite four or you can make a champion of your own. That's the pairing I'm looking for. I'd like to keep the pokemon teams minimal so one or two at most for each of them. I've yet to figure out a system for their battles yet but I'd like to try using pokemon showdown to simulate some of them. If that's not convenient then we can work out how the battles will play out another way.
I'd like to play this in an episodic way, meaning there'll be probably a few time skips and showing only when the pair cross paths. So things might need explaining behind the scenes. Working up to something that's bigger than just the two of them. It'll be difficult to top almost destroying the world, and time and space etc. While these two are fighting constantly and maybe sometimes using dirty tactics on each other, like catch and release after some teasing and all the good stuff, the other gangs could form one solid group (Plasma I think should be divided on the issue, those loyal to Ghetsis should side with the gangs and the ones Loyal to N could side with the champions) ready to strike. Some could be planted in positions of power, then the grunts pretty much muscle their way into getting things done while the higher ups plan and put a stop of police activity in their areas.
The short of it meaning war between the champions and the gangs , bringing the whole world with them. Bailey would be unaware of all the shadow meetings going on and Rocket largely would be left out of it, other than the grunts hired by the other teams. Bailey could pull her team either way but the fun is in getting to that decision after the more light stuff with her champion.