Mewtwo Strikes Back
As the title might suggest, the first Pokémon movie is about Mewtwo "striking back" against the humans that created, used, and betrayed him.
Mewtwo Strikes Back is a very powerful tale, describing what it is to wake up and be told you are nothing more than a science experiment, and that, philosophically speaking, you should not even exist. Mewtwo breaks out from under control of both the scientists who created him and Giovanni, the leader of Team Rocket who had financed Mewtwo's creation and sought to control the most powerful Pokémon to ever exist. Once Mewtwo is on his own, he decides prove his worth as a living being; to do so, he will battle and defeat Mew (thereby proving he is not inferior to the source of his DNA), wipe out the human race (for creating him), and by replacing all the original Pokémon with clones (for he feels clones should rule the earth).
By the end of the movie, Mewtwo realizes that just because he is a clone doesn't mean he is any less worthy, powerful, real, or respectable as a naturally-born "original." He also recognizes that not every human is bad, and, clone or not, what really matters is how one lives one's life.
The dubbed version was a bit watered down from the Japanese version, but it is still enjoyable to watch.
Prequels and SequelsIn Japan, several promotional tie-ins were created, coinciding with the theatrical and later home video release of the film, and each attempted to shed some more light on Mewtwo's back-story. These prequels were each very different from each other, and most were never released outside of Japan.
Much later, this story of Mewtwo was continued in the special episode Mewtwo Returns.