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The film focuses on Celebi who travels to the future and brings with a boy named Sam when being chased by a hunter. Meanwhile Ash, Misty, Brock, Pikachu and Togepi are on their way to the next gym in their Johto journey and get a lift from a man named Maki who takes them to his hometown of Arborville.

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.

In Alamos Town, a large shrine to Dialga and Palkia, the Space-Time Tower, sits. But when Dialga and Palkia begin to battle in their dimension, the fight spills over into the Pokémon world, trapping Alamos Town away from the rest of the world.

When dark, poisonous clouds begin to appear in the Reverse World, home to Giratina, it takes matters into its own hands and pursues the cause of the clouds: Dialga and Palkia. Finding Dialga, it lures it for revenge, and assumes Shaymin to also be responsible.

Ash is a young boy who has always dreamed of becoming a Pokemon trainer. At age 11 he is gifted his first Pokemon, Pikachu, from Professor Oak.