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).

Mima leaves the idol group CHAM, in order to pursue her dream as an actress. Mima climbs up the rocky road to success by performing as rape victims and posing nude for magazines, but is haunted by her reflections of the past.

Pikachu and the gang learn responsiblity, team work as well as cooperation during their Summer vacation at Pokemon Island.