2nd Gen Giovanni and the Master Ball

As we all know: in some point of the game you have to enter Silph Co, fight your way through hordes of Team Rocket members, get to their boss Giovanni and finally are able to free the innocent employees. As a reward you would get the prototype of the Master Ball, the only Master Ball in the whole game. With it you are able to catch every Pokemon you want. Giovanni himself flees to his gym in Viridian City in order to rebuild Team Rocket secretly. Unfortunatle bevor he can do so, the player enters his gym and beats him once and for all. That's how the story unfolds in Generation one of the games.

But, what if this Master Ball wasn't the only one? What if Giovanni managed to escape with some of them, what would he have done?

On a side note: in the anime Giovanni was in possession of Mewtwo, he even destroyed Garys whole team in a blink of an eye.

Considering free space wasn't that limited and so, there could have been more content, than they implemented: how could have the story unfolded, if they made the decision to give Giovanni at least one Master Ball?

Maybe he went to Cerulean Cave, catched Mewtwo (the player follows him, but couldn't do anything to hinder him) and takes it to his gym (rebuilt as a laboratory). There the player would be forced to fight Giovanni and his Mewtwo, finally beating him, while Mewtwo flees. Team Rockets plans failed and the player gets his last badge.

In the after game you were able to find Mewtwo in Cerulean Cave, finally able to catch it.

So, what's your thoughts? How could the story have unfold?

I think it'd make for an interesting plot if there was ever a sequel to G/S/C. With Giovanni being a much more worthwhile fight. I could see him controlling people with Mewtwo's psychic powers and creating thunderstorms to take over the world.

well seems cool but i think it would fit g/s/c better. while red was busy training in mt.silver gold would fight giovanni who was trying to catch Mewtwo for the past 3 years for the last badge against Mewtwo. but it would be cool with r/b/y too.