The Cloned Pokemon are Pokémon created by Mewtwo in MS001: Pokémon The First Movie - Mewtwo Strikes Back. They appear again with their creator in Mewtwo Returns.
Having been created through Dr. Fuji's cloning experiments to surpass Mew, Mewtwo came to believe that cloned Pokémon were superior to normal Pokémon, who had shamed themselves by serving humans. He thus determined to destroy humans and natural born Pokémon alike and replace them with an army of clones. To this end, he invited a number of trainers to the rebuilt cloning facility on New Island. After proving the superiority of his first three creations-cloned version of a Venusaur, Blastoise, and Charizard-against natural versions of each, Mewtwo proceeded to capture most of the trainers' Pokémon using special Poké Balls. He then cloned all the Pokémon captured, but was then challenged by the original Pokémon under the leadership of first Ash Ketchum and then Mew. In an effort to prove the superiority of the clones, Mewtwo suppressed the special abilities of the other Pokémon using his psychic powers, and the two sides entered into a fierce battle. It finally ended when Ash tried to intervene and was gravely harmed, only to be revived by the tears of natural and cloned Pokémon alike.
Having seen the error of his ways, Mewtwo erased the memories of the humans and Pokémon who had been caught up in his schemes and departed for the Johto region with the clones. They settled in a wilderness area, but were eventually found by Mewtwo's former "master" Giovanni. Giovanni threatened the clones in an effort to force Mewtwo to serve him once again. Fortunately, his efforts were thwarted by the arrival of Ash and his friends, and Mewtwo was able to erase the memories of Team Rocket regarding the clones. With that, the clones went their separate ways in order to live as Pokémon in the wild.