Tarina alkaa yksityisetsivä Harry Goodmanin mystisestä katoamisesta. Hänen 21-vuotias poikansa Tim lähtee selvittämään tapahtumia apunaan Harryn entinen Pokémon-työpari, suloinen ja hulvaton vitsiniekka, etsivä Pikachu. Huomattuaan heidän ainutlaatuisen kykynsä ymmärtää toisiaan he lähtevät huimaan seikkailuun selvittääkseen mysteerin. Yhdessä he etsivät vihjeitä neonvalojen alla sykkivässä modernissa metropolissa, Ryme Cityssä, jossa ihmiset ja Pokémonit elävät rinnakkain. Matkansa varrella he tapaavat monenlaisia Pokémoneja ja saavat selville katalan juonen, joka uhkaa tuhota rauhallisen yhteiselon ja koko Pokémon-universumin.
Tarina Koko, Pokémonin kasvattama nuori poika, ja uuden siteen luominen ihmisten ja Pokémonien välille.
Ash meets the Mythical Pokémon Volcanion when it crashes down from the sky, creating a cloud of dust—and a mysterious force binds the two of them together! Volcanion despises humans and tries to get away, but it’s forced to drag Ash along as it continues its rescue mission. They arrive in a city of cogs and gears, where a corrupt official has stolen the ultimate invention: the Artificial Pokémon Magearna, created 500 years ago. He plans to use its mysterious power to take control of this mechanical kingdom! Can Ash and Volcanion work together to rescue Magearna? One of the greatest battles in Pokémon history is about to unfold!
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.
Ash, Pikachu ja muut tutut hahmot jatkavat taivallustaan elokuvassa, joka on jo sarjan 11:s. Tällä kerralla seikkailu sijoittuu vaihtoehtotodellisuuteen, jossa painovoimakin toimii satunnaisesti. Tämä avaa ikkunat piirtäjien mielikuvitukselle, ja elokuva onkin aiempia visuaalisempi. Juonesta ei saa tolkkua kuin Pokémon-maailmaan perehtynyt asiantuntija.
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 by a violent group of Hellgar. 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 Wave Bomb, he eliminated them. Though by the threat, the queen of Rota, Lady Rin was resolute to die with her civilians, and so Arlon made a choice.
Deoxys, a Pokémon from outer space, terrorizes the high-tech city Ash Ketchum and his friends are visiting.
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.
Little monsters run amok at a heavy metal festival.