>>38780430Being a gangster, you can coerce civilians– you obviously have to beat Pokémon Trainers to do this– into letting you take their Pokémon and possibly other stuff. You’ve got a civilian guise you can take on so you won’t be spooking people 24/7, though Poké Balls are considerably more limited than they are in the “real” games. Catching Pokémon is possible, but you don’t snag them during battle. It is thus encouraged to steal trainers’ Pokémon; a “goody-goody” run without doing so is difficult but possible.
The story is more or less driven by a chain of assignments you’re given as you climb Team Rocket. Being the boss’s son, Silver plays into the story at some point, definitely later on. Red, Blue, and Leaf also all appear as “rival” characters, and all four can be named. Blue fights you the least since he’s focusing on the League and the Dex too much, Leaf fights you the most since she’s not as focused on the League as Red and Blue are. Red and Blue are seen together and Blue and Leaf are seen together, but not Red and Leaf.
Johto and the Sevii Islands are ideally both accessible, and mons that appear in Kanto in GSC and their remakes (like Houndour, Murkrow, and Slakoth) show up in Kanto. Silver is probably in Johto; I imagine you're sent there to scoop him up and take him to to the boss or something. Maybe one more path from Kanto to Johto, like between Blackthorn and Pewtwer, so there’s a way other than Tohjo Falls or the magnet train. The hideouts in Celadon, Mahogany Town, and on Chrono Island are all used, but you
don’t go into Giovanni’s personal hideout in the Viridian Gym
until the very end.
TL;DR: Vento Aureo with Pokémon.
I made a text-based mockup intro to the game in Twine a while back, I’ll post it if anyone’s interested 