The year is 2071. Following a terrorist bombing, a deadly virus is released on the populace of Mars and the government has issued the largest bounty in history, for the capture of whoever is behind it. The bounty hunter crew of the spaceship Bebop; Spike, Faye, Jet and Ed, take the case with hopes of cashing in the bounty. However, the mystery surrounding the man responsible, Vincent, goes deeper than they ever imagined, and they aren't the only ones hunting him.
In the legendary past, before Poké Balls were invented, an aura-guiding hero Pokémon named Lucario sensed two groups of armies about to clash, and a threat of a massive war in front of Oldoran Castle in Kanto that would leave no survivors. He transferred this message to his master, the legendary hero Arlon, while he was being attacked by a violent group of Hellgar. During the battle, his sense of sight was lost and he was rendered unable to see. He used the detection of his Aura, and so with the offensive Wave Bomb, he eliminated them. Though by the threat, the queen of Rota, Lady Rin was resolute to die with her civilians, and so Arlon made a choice.
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.