|Ash Ketchum, Brock and Dawn are on their way to a Pokémon championship in Crown City but rescue the shapeshifting, mischievous Zorua from a group of Vigoroth, Zorua able to speak English 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, touching it reverting Zorua to normal. The next day, Celebi appears in town and causes all the flowers to bloom, much to the delight of several townsfolk, who recall a mysterious event that happened twenty years when all the plant life died.|
Meanwhile, businessman Grings Kodai unleashes the imprisoned Zoroark upon the city, pretending to hold Zorua prisoner. Kodai is aided by his assistant Rowena and bodyguard Goone. Zoroark uses her illusion powers to take the form of Raikou, Entei and Suicune and scare the townsfolk; Kodai editing 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, caused by an encounter with Celebi twenty years ago where he touched the Time Ripple, created when Celebi time travels, gaining his powers of foresight, causing the destruction of the town’s plants in the process. Kodai is looking for the Time Ripple again, 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 befriends Zorua, Pikachu and Piplup. Ash and co. are captured by Kodai, but Rowena releases them, actually Karl’s fellow journalist working undercover to find out Kodai’s plan.
Rowena explains Kodai’s past, and how the Time Ripple will linger for a day after Celebi time travels, Kodai planning to absorb its power again to replenish his fading foresight. Kodai has a vision that Celebi will show him the Time Ripple, and he targets it and Zorua. Zoroark escapes her prison, just as the real Legendary Beasts arrive in town and engage Zoroark in a fight. Kodai harms Celebi, seeing more of the future. Ash and co. arrive, Kodai realising Rowena is the woman in his vision. The group flee with Zorua and Celebi, meeting up with Joe and Tammy, Joe revealing the location of the Time Ripple is in the local stadium, Kodai eavesdropping on the conversation and races for the stadium. While Karl and the others stop the fighting between Zoroark and the Legendary Beasts, Ash, Dawn, Brock, Pikachu, Zorua and Celebi head for the stadium.
Dawn and Brock fight Goone and his Pokémon, aided by Zoroark, who then join Ash and co. at the stadium. Kodai takes Zorua captive and threatens to kill it unless the heroes back off, before absorbing part of the Time Ripple and replenishes his power, gloating about how he has fooled the townsfolk twice with his media manipulations. However, Zoroark reveals it was an illusion she created, Karl and Rowena revealing they have recorded Kodai’s gloats. Kodai tries to kill Zoroark, but fails. Kodai tries to reach the Time Ripple but is blocked by the Legendary Beasts, and his attempt to escape fails.
Zoroark dies from exhaustion, but Celebi ventures into the Time Ripple to rejuvenate its own power and revives Zoroark, before departing back to the future. Kodai’s confessions to his crime are played on television, and he is promptly arrested. At the end of the film, Zorua and Zoroark depart back to their homeland, the Unova region, with Karl and Rowena for company. Ash promises Zorua that he and Pikachu will reunite with it when they visit Unova some day.