40 years ago, a Pokemon Hunter attacked a Celebi. Fortunately, a young boy named Sammy came to its rescue. With its Time Traveling ability, Celebi transported itself and Sammy to the future. There, Ash, Misty, and Brock helped Sammy take Celebi to the healing lake in the forest so it could recover from its injuries. However, an evil Team Rocket member named Viscious a.k.a. "The Iron Masked Marauder" tried to capture Celebi using his technology. As Ash and his friends attempted to escape, they encountered Jessie, James, and Meowth, who also wanted to catch Celebi. The race was on to get Celebi and Sammy back to the forest before Viscious could use Celebi to destroy it and themselves.
The film chronologically takes place after episode 205 of Pokemon.
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