Gladion

The Team Rocket leader, Giovanni, has found Mewtwo in a remote area of the Johto region. As Giovanni tries to re-capture Mewtwo, Ash and his friends are kidnapped by Domino, a new Team Rocket member, while trying to rescue Pikachu from Jessie and James.

Dr. Fuji, a research scientist of Team Rocket, briefly describes in a prologue how his researchers uncovered a fossil of the remnants of Mew, one of the rarest Pokémon in existence, believed to be extinct (although this is not the case).

The film's setting is in the water-themed Johto city of Altomare (which means "High Sea"), based on Venice, Italy. The city is watched over by two legendary Pokémon, Latias and Latios.

The story revolves around the Millennium Comet, which appears in the night sky for seven days once every thousand years. It is, at the same time, when the legendary Pokémon Jirachi awakens from a long slumber to absorb the comet's energy.

Lucario and the Mystery of Mew opens over the foggy landscape of Rota, with Ho-oh flying overhead. Then it goes to Lucario, who is jumping from rock to rock.

One night out at sea, a mysterious Pokémon egg washes into a massive ship led by Phantom the Pirate. As Phantom is about to hatch the egg for his desires, one of his ship employees steps in, snatches the egg, and escapes the ship, being none other than a Pokémon ranger using his capture styler to make a clean getaway with a Mantine.

10-year-old Satoshi, after finding a Pikachu messing with the wiring in his house, is on a journey to become the greatest Pokemon Master and to beat out his rival, Shigeru. Along the way, he meets with many other Pokemon trainers and advisors, including water-based trainer (and gym leader) Kasumi, ground- and rock-based trainer (and gym leader) Takeshi, and others.

The story begins with Yggdrasil, a popular online game which is quietly shut down one day; however, the protagonist Momonga decides to not log out. Momonga is then transformed into the image of a skeleton as "the most powerful wizard.