a scientist working on cloning pokemon has somehow cloned mew into mewtwo but it destroys the lab so giovanni uses its power for it but than mewtwo escapes and wants revenge on all humans. meanwhile ash battles a trainer who even uses a donphan (a johto pokemon) watching it mewtwo sends an invitation to new island to meet the strongest trainer but the boat service stops so only ash and 3 other trainers get to the island (well misty brock and team rocket also get there). there a mising pokemon center nurse is revealed to have been helping mewtwo through the situation and mewtwo after beating the final kanto starter forms takes the pokemon to clone using dark balls pikachus the last one standing but ash isn’t able to save it directly but does eventually destroying the machine and freeing the pokemon leading to an endless showdown between the clones and the pokemon (except ash’s pikachu team rocket’s meowth and the clone meowth) battle each other as well as mew battling mewtwo with no end in sight ash gets in the way of the attacks sacrificing himself but the tears of the pokemon bring him back to life and convinces mewtwo that there is good in humans and he sends them off the island removing their memories ending the movie.