I guess those old theories were true.

Giovanni invaded Silph Co to steal the Master Ball because he wanted a way to contain Mewtwo.
Team Rocket stole the Silph Scope and attacked Pokemon Tower to arm themselves with Ghost Types to battle him with.

Seems like in the universe he won, he mass produced Master Balls and supplied them to his team, judging by how he and the rest of the Team leaders use them even for their common mons, and his ultimate plan is to catch an army of Ultra Beasts

He probably went after Lysander specifically for his Mega Evolution research, thus getting Mewtwo's Mega Stone