Pokemon Trainer Red is so awesome he foiled Giovanni's plan before it started.
In Mt. Moon, the Rockets were trying to resurrect ancient, powerful fossil Pokemon. You stop them there and take one yourself.
At Celadon and Pokemon Tower, Team Rocket was trying to use the Silph Scope to catch Ghost-type Pokemon, which Psychic-types are weak to. You stop them there and take the Silph Scope, rescuing Mr. Fuji.
At Silph Co., [=NPCs=] say that Giovanni is after the Master Ball, which can catch any Pokemon. You stop him there and get it yourself.
Giovanni is revealed to be the Viridian Gym Leader and possesses the Earth Bade, which makes any Pokemon obey you.
All that evidence points to one thing. Giovanni was trying to weaken and capture Mewtwo to rule the world, and Red stopped him before he could begin.