In this film, we meet the new Pokémon, Celebi, who has the power to travel through time. Vicious, the future descendant of James and Jessie of Team Rocket, travels back in time to wreak havoc, and it's up to young Ash, Pikachu and friends to stop him. Along the way, Ash continues to mature into the unstoppable Pokémon trainer he will become in the future.

An evil genius in a flying fortress is trying to kidnap the birds of the fire, ice, and lightning islands in hopes of luring the sea power, Lugia, and controlling the world. Ash and his friends, in the process of carrying out an island tradition that requires visiting those three islands, discover the plot and try to stop it. Even the comic villains, Team Rocket, turn good and help out in the end against the threat of world destruction. And Pokemon assemble from all around the world in case they can be of help (but they end up helping only the merchandising).

High school student Ling Xiaoyu is recruited by Anna Williams of G Corporation to transfer to Kyoto University and gather information on a student named Shin Kamiya. Meanwhile, Jin Kazama, the current head of the Mishima Zaibatsu, sends Alisa Bosconovitch to the university for the same mission. Though they do not know each other's true motives, Xiaoyu and Alisa become close friends. However, their friendship is put to the test when Shin is captured by an unknown assailant.