The film starts with the creation of Mewtwo, a genetically enhanced Pokemon created from the DNA of Mew, the rarest Pokemon ever. The scientists are thrilled that their test has succeeded after so many failiures, but Mewtwo isn't happy about being just a guinea pig and destroys the lab with its incredible psychic power. Giovanni, the boss of Team Rocket befriends Mewtwo and helps him enhance his power, but then he tries to use Mewtwo for his own ends and the Pokemon decides that all humans are evil, and there Pokemon are just slaves. Then Ash and some other trainers get a message asking them to go to an island but there is a storm. Only a few, including Ash, Misty and Brock make it, only to discover it is Mewtwo trying to clone their Pokemon and use the clones to conquer everyone. The Pokemon all fight their clones and Mew shows up and fights Mewtwo. Then Ash tries to stop the fight and gets killed when he is hit by Mew and Mewtwo's attacks, but the tears of all the Pokemon revives him and Mewtwo decides that humans aren't all bad.
Trivia: The "fighting is wrong" moral ending exists only in the American version. In the original Japanese, the ending was that Mewtwo accepted it could be a proper Pokemen in spite of having been brought to life by humans, because Ash (Satoshi in the original Japanese) is still a proper human in spite of just having been brought (back) to life by the other pokemon.Moose
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