The devious leader of Team Rocket Organization, Giovanni, has a fervent ambition to take control of the Pokémon world through both financial and military means. To achieve his military needs, he covets a Pokémon stronger and more adept than any other, a veritable living war weapon, so he enlists a scientist named Doctor Fuji to create this being from the DNA of the ancestor of all Pokémon and most powerful of Pokémon, Mew, which Fuji had found on a previous jungle expedition. Fuji accepts, for he is heavily into the prospect of cloning to create and restore life itself, because of his love for his deceased daughter, Amber.

Lina Inverse and her sidekick Naga the Serpent are happily enjoying lunch when the entire town ducks under cover before an invasion of Marlene Culvert and her legion of bloodthirsty dragons. The cause of the invasion? Marlene is in a feud with her father, the king, over her allowance. Lina leaps into action to defend the village against Marlene, her tetrad knights and her dragons, but her dependable Dragon Slave spell fails her. Right when she thinks she has won, the real battle has just begun.