The adventure explodes into action with the debut of Mewtwo, a bio-engineered Pokémon created from the DNA of Mew, the rarest of all Pokémon. Determined to prove its superiority, Mewtwo lures Satoshi, Pikachu and others into a Pokémon match like none before. Mewtwo vs. Mew. Super-clones vs. Pokémon. It's the ultimate showdown ... with ...

40 years ago, a Celebi was being attacked by a Pokemon Hunter. Luckily, a young boy named Yukinari saved Celebi. Using its Time Traveling power, Celebi transported itself and Yukinari 40 years into the future. There, Satoshi, Kasumi, and Takeshi assist Yukinari to the healing lake in the forest so they can heal the wounded Celebi. Unfo...

Ash and friends (this time accompanied by newcomer Dawn) arrive at an idyllic village on their way to their next Pokemon contest, where chaos will soon erupt with the prophecy of two Pokemon Gods (Dialga and Palkia) and the arrival of a mysterious, seemingly deadly Pokemon named Darkrai, which has the power to distort space and time.

In the legendary past, before Poké Balls were invented, an aura-guiding hero Pokémon named Lucario sensed two groups of armies about to clash, and a threat of a massive war in front of Oldoran Castle in Kanto that would leave no survivors. He transferred this message to his master, the legendary hero Arlon, while he was being attacked ...

Satoshi, Kasumi, and Takeshi continue exploring the Johto region, then have to rescue Pikachu after Musashi and Kojiro kidnap him. The search leads them to the hidden plateau where Mewtwo has established a haven for the cloned Pokémon from the previous film. The evil Sakaki is plotting to recapture Mewtwo and renew his efforts to creat...