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).

The Evangelion saga from TV is artfully recounted, with some additional scenes, in part one see: "Shin Seiki Evangelion" (1995) Part two starts immediately afterward, where the NERV organization has outlived its usefulness. The shadowy covenant of SEELE launches an all-out commando assault against the ill-defended headquarters. Asuka, semi-comatose, is placed in her EVA for safety, while Misato and company struggle to find Shinji and Rei before they're assasinated by SEELE's forces.

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

Ash, Pikachu and the rest of the Pokemon gang try and stop a pair of thieves hiding out in the canals and alleyways of Alto Mare, the water capital of the world. Joining the adventure are two new Pokémons, a brother/sister pair named Latias and Latios who are protecting the Droplet of the Heart - a valuable treasure.