40 years ago, a Celebi was being attacked by a Pokemon Hunter. Luckily, a young boy named Yukinari saved Celebi. Using its Time Traveling power, Celebi transported itself and Yukinari 40 years into the future. There, Satoshi, Kasumi, and Takeshi assist Yukinari to the healing lake in the forest so they can heal the wounded Celebi. Unfortunately an evil Team Rocket member, Vicious, tries to capture Celebi using his technology. As Satoshi and Co. try to get away from Vicious, they also run into Musashi, Kojiro, and Nyarth, who also want to capture Celebi. Soon it becomes a race against time to get Celebi and Yukinari back to the forest before Celebi is caught and is used to destroy the forest and themselves.