Prior to the movie, businessman Grings Kodai discovered Celebi in Crown City and used his Pokémon to attack and knock out the Time Travel Pokémon when it tried to escape through the Ripple of Time. Kodai then touched the time ripple that was produced due to Celebi's time traveling, and as a result of this, he gained the ability to have powerful visions that show him the future. However, by touching the time ripple, he caused the flow of time to reverse in Crown City, destroying all of its greenery.
Twenty years later, Celebi returns to the city, unaware of the fact that Kodai wished to capture it in order to renew his ability to see into the future. While greeting some of the local Pokémon and making some of the greenery grow, it meets and befriends Zorua while the latter was searching for his mother, Zoroark, who was being blackmailed by Kodai. After calming a large group of angry wild Pokémon that were about to attack Zorua in retribution for what his mother was forced to do, Celebi agrees to assist its new friend in locating his mother. During their search, Celebi comforts a saddened Zorua by growing a patch of grass around him that reminded Zorua of his mother's fur.
Soon, Celebi finds itself and Zorua pursued by Kodai's minions. During the confrontation, Zorua tries to protect Celebi but is easily defeated. Kodai quickly captures Celebi and strangles it in order to force it to reveal the location of the Ripple of Time to him. Zorua recovers and tries to fight again, only to be overwhelmed until Ash and company arrive and rescues them both. Celebi is left too badly hurt to fly, and thus it's up to Ash and the others to get it to the time ripple before Kodai. However, Kodai is quickly on their tail, forcing Dawn and Brock to stay behind to hold off Goone, but Kodai still close behind. Thinking quickly, Celebi hides in Ash's backpack, allowing Zorua and Karl's Bronzor to lure Kodai away.
Ash and Pikachu manage to get Celebi into the Pokémon Baccer World Cup Stadium, the location of the Ripple of Time, but Kodai, having defeated and captured Zorua, arrives and disables the group with his Mismagius's Psychic. Zoroark arrives, but is likewise detained when Kodai threatens Zorua's life. Unopposed, Kodai then finds what he believes to be the time ripple, and begins to absorb its power, not caring if the disaster that befell Crown City years ago occurred again. The "time ripple" ends up being an illusion created by Zoroark and Kodai was nowhere near the energy field. Afterwards, Kodai was driven away by Zoroark and the guardians of Crown City, but Zoroark collapses from mortal wounds sustained from Kodai. As Zorua cries over his mother, Ash helps Celebi reach the true Ripple of Time, allowing it recover its strength. Celebi then uses the ripple's energy field to heal Zoroark, repaying Zorua for his kindness. Happy that Zorua and Zoroark are reunited and Kodai was defeated, Celebi makes the area's greenery bloom in celebration before finally departing for another time, with Zorua promising to be its friend forever.
In the credits, Celebi is last seen emerging from the time ripple and disappearing into the depths of a forest.
