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

On their way through the Battle Frontier, Ash and friends meet up with a Pokémon Ranger who's mission is to deliever the egg of Manaphy to a temple on the ocean's floor. However, a greedy pirate wants the power of Manaphy to himself.

40 years ago, a Celebi was being attacked by a Pokemon Hunter. Luckily, a young boy named Sammy saved Celebi. Using its Time Traveling power, Celebi transported himself and Sammy 40 years into the future. There, Ash, Misty, and Brock assist Sammy to the healing lake in the forest so they can heal the wounded Celebi. Unfortunately an evil Team Rocket member, Viscious a.k.a. "The Iron Masked Marauder", tries to capture Celebi using his technology. As Ash and Co. try to get away from Viscious, they also run into Jessie, James, and Meowth, who also want to capture Celebi. Soon it becomes a race against time to get Celebi and Sammy back to the forest before Celebi is caught and is used to destroy the forest and themselves.

The movie features Ash and his two friends Iris and Cilan, as they help a Keldeo battle against a powerful Dragon-type Pokémon named Kyurem as his test to become a Sacred Swordsman.

In the legendary past, before Poké Balls were made; 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 Cameron Palace in Kanto that would leave no survivors. He transferred this message to his master, the legendary hero Sir Aaron, while he was being attacked by a violent group of Houndoom. During the battle, his sense of sight was lost and he was rendered unable to see. He used the detection of his Aura, and so with the offensive Aura Sphere, he eliminated them. Though by the threat, the queen of Cameroon, Lady Rin was resolute to die with her civilians, and so Sir Aaron made a choice.

Satoshi, Haruka, Takeshi, and Masato come upon the festival of the Wishing Star of Seven Nights. During their enjoyment, the legendary Pokemon--Jirachi, decends from the heavens and befriends Masato. Jirachi, with the power to grant any wish, is sought after by many people wanting to claim its power. One man seeks to use its legendary power to revive an ancient pokemon known as Groudon, unaware of the dangers hidden within Jirachi's powers