i've wanted this since the start, when the guy on nugget bridge asks you to join. i guess if it wasn't in a new region, you'd play through the first two gens from the other side, beating the gym leaders and important businessmen and whoever into submission and taking over the entire region, looting equipment, stopping whatever that police guy on the boat was doing, infiltrating all the labs and institutions through battle or bribery. i guess starters would probably be koffing, ekans, or meowth, but it could be interesting if you start with rattata or zubat and work your way up from powerless grunt to trusted executive. there could be side plots involving pokemon experiments like the lake of rage stuff, where you recruit scientists from the lab and museum, activate machinery from the burned mansion and power plant, and create powerful clones and forced evolution. of course stealing pokemon and items would be pretty core. maybe they wouldn't let you buy from shops at all, without a disguise.