This for gen 1 & 2

There is some sort of war, nvm how it starts. Mons are used to fight in war (Lt surge). Most adults die from war, only old people, woman and children left.

Some point after the war...

Sillph co owns everything = megamonoply. This is why only 1 store in any given city. They own pokemart and pokecenters, they own the gyms and use them as recruiting centers. They gain power after acquiring the patents to digitization of matter (PC system + Pokeballs) from young prodigy Bill. They set up Bill with a cushy pad in countryside (Kanto, Cerulean) to continue his research, more on that later.

Several years (20?) before start of Red/Blue mew discovered in Guyana by either independent researchers or people working for Silph. Most likely the latter. In any case Silph finds out about it tries to weaponize it. Mewtwo created through genetic engineering.

Meanwhile, Giovanni creates a rogue revolutionary group trying to over throw the totalitarian Silph co, he does this in secret while climbing rank to gym leader. Calls it Team Rocket.

At some point Giovanni finds out about Mewtwo, realizes its power and tries to break it out. Mewtwo gets loose kills some people, flees to Cerulean, beyond the powers of both Silph and Giovanni.

Exposed, Giovanni makes his move and starts terrorizing Silph. Gathering resources and recruits (Mt Moon, Cerulean) and eventually attacking Silph headquarters.

This is where main character comes in. Silph sends word to Oak to choose viable candidates to join their ranks. Oak chooses his grandson and main character. Gives them pokedex to catalog mons left after the war as a pretext. Gym leaders help train and guide the main character for the match against Team Rocket.

Ofc, it works. Main character collects gym badges without a second thought, finds Team Rocket at Silph, promptly dispatches them.

This is where it gets interesting. Silph still has a serious problem, the one they've had all along: Mewtwo (con in next post)