Ash Ketchum, Brock and Dawn are at a Pokémon Center watching a Pokémon Baccer match on TV. Ash and co. are intrigued by the match and decide to head to Crown City to watch the Pokémon Baccer World Cup.
Meanwhile, famous businessman Grings Kodai, his henchman Goone and secretary Rowena are in Unova where they find Zoroark and a sleeping Zorua. They capture the two Pokémon and take off for Crown City. Zorua, who is trapped on Kodai’s plane, manages to escape and disguises itself as a Skiploom, and drifts down to the ground unnoticed. The protagonists are on their way to the Pokémon Baccer World Cup in Crown City, and encounter and rescue the Zorua from a group of Vigoroth. Zorua is able to speak to humans through telepathy. Zorua wishes to go to Crown City to find its mother Zoroark who it refers to as “Meema”. Zorua’s shapeshifting skills are compromised by the constant presence of its tail. The next day, Celebi appears in town and makes all the flowers to bloom, much to the delight of several townsfolk, who recall a mysterious event that happened twenty years where all the city’s flora died.
Kodai then unleashes the imprisoned Zoroark upon the city, pretending to hold Zorua prisoner. Zoroark uses her illusion powers to take the form of Raikou, Entei and Suicune and scare the townsfolk; Kodai edits recorded footage of her to make it look like the fake Pokémon are on the rampage and labels Zoroark as evil. Ash, Dawn, Brock and Zorua arrive, seeing Zoroark on television, Zorua trying to reach the cut-off town. They meet Karl, a local journalist investigating Kodai, who leads them into town through a hidden passage in a windmill. Kodai is revealed to be able to see into the future. Kodai looking for something called the Time Ripple to gain the power of foresight, and has Goone recapture Zoroark, having a vision that Ash, Dawn, Brock, Karl and an unknown woman will stop him.
The group meet Karl’s grandfather Joe and his friend Tammy, who explain Celebi used to visit the town before the plant life died. Zorua runs off on its own to find Zoroark, finding the other Pokémon are hostile towards it, but Celebi appears and befriend Zorua, Pikachu and Piplup. Ash and co. are captured by Kodai, but Rowena releases them, revealed to actually be Karl’s fellow journalist working undercover to find out Kodai’s plan. Rowena explains Kodai’s past; how the Time Ripple is created after Celebi time-travels and will linger for a day. Kodai planning to absorb its power again to replenish his fading foresight, that will cause destruction of the town’s plant life in the process, like Kodai did twenty years previously.