Okay, so let me get this straight.
Giovanni funds Dr.Fuji's cloning project to make the worlds strongest pokemon, Fuji can work bringing his daughter back to live and get some cash and Giovanni gets mewtwo.
YEARS of SECRET research on an island gets destroyed when mewtwo goes wakes up early and goes berserk, leaving no survivors.
Giovanni then trains mewtwo, they have a falling out and Giovanni's lab is also destroyed.
Ash and Co. meet this mewtwo and later they forget everything to meet him in johto and not forget everything.
Then in movie prologues we see mewtwo being batman watching over cities, possibly following Ash.
THEN when they are about to become road kill by super sonic bugs mewtwo comes and saves them BUT this mewtwo was made somewhere else has nothing to do with anything in the series.
GF better have a real good explanation, Like after the events of Returns Giovanni says fuck it and tries to make his own which would explain the slight change in looks.
