>>21084486It's implied by the various location s you see and battle Giovanni and it all coincides with the first movie.
The whole reason Giovanni was ever at Pokemon Tower in Lavender town was to get to Mr. Fuji who helped Team Rocket work on Mewtwo which is only reinforced by the movie until...
Giovanni is in Silph Co. for what now? The Masterball, right? but WHY does Giovanni need the Masterball? It's to catch Mewtwo who -back then- was the most powerful Pokemon. He didn't wan Mewtwo because he heard about it through the grapevine. He wanted Mewtwo because he had Professor Fuji and his team of scientists to MAKE the most powerful Pokrmon for him to use. Mewtwo broke out, and was alive and by technicality was a successful experiment. That's millions of $poke in research that he spent on a Pokemon that ran away to go hide in a cave because it feared it'd own power.
If I was Giovanni I'd be bitter as fuck. So I would go interrogate Fuji for Mewtwo's whereabouts, and I'd then invade Silph Co. for the ONE Pokeball that was able to catch any Pokemon without fail.
And then, of course you have The Game Corner serving no more of a purpose than to be a base of operations.
But basically, it's HEAVILY implied what Giovanni is trying to do just by the order in which you face him and his whereabouts.