Crown City once existed in perfect harmony with the forest. Twenty years ago, a man named Grings Kodai absorbed the Time Ripple, created by the time-travelling Pokémon visiting the city, Celebi, to gain the power to see into the future. This caused nearly all of the city’s greenery to die. With his power, Kodai became a successful businessman and controlled the mainstream media. Over time, the people and Pokémon worked together to bring the city back to life.
In the present, when his visions begin to fail, Kodai plans to absorb the power of the ripple, once again destroying the city’s greenery, before the ripple disappears. He captures the Pokémon Zoroark and the Zorua it takes care of, and transports them across the sea on Kodai’s aircraft headed to Crown City. Zorua uses its illusion powers to escape. The Pokémon trainers Ash Ketchum, Dawn, and Brock find Zorua in the forest outside the city and accompany it to Crown City to reunite it with Zoroark.
Kodai unleashes the imprisoned Zoroark upon the city, pretending to hold Zorua as a hostage. Zoroark uses its illusion powers to take the form of Entei, Raikou, and Suicune, the guardian protectors of the city in ancient times, scaring the townsfolk. Kodai and his secretary Rowena manipulate the footage to fabricate news that Zoroark is evil and causing the guardian protectors to rampage, and orders the city to be sealed off while he searches for the Time Ripple in secret. Ash, Dawn, Brock, and Zorua meet Karl, a local journalist investigating Kodai. Karl leads them into the sealed-off part of the city through a sewer. Kodai has his henchman Goone recapture Zoroark, and has a vision that Ash, Dawn, Brock, Karl, and Rowena will stop him.
Zorua, followed by Ash’s Pikachu and Dawn’s Piplup, runs off to find Zoroark, but Celebi appears and befriends Zorua, Pikachu and Piplup. Kodai captures and imprisons Ash, Dawn, Brock, and Karl. Rowena, revealed to be an undercover journalist investigating Kodai, releases them. Kodai has a vision that Celebi will show him the Time Ripple, and he targets it. Kodai harms Celebi, seeing more of the future. Ash, Dawn, Brock, Karl, and Rowena flee with Zorua and Celebi, meeting up with Karl’s grandfather Joe and his friend Tammy. Joe reveals that the Time Ripple is near a countdown clock in the local stadium; Kodai eavesdrops on the conversation.
Meanwhile, Zoroark escapes its imprisonment. The real guardian protectors arrive to fight Zoroark, believing it is attacking the city. Karl, Rowena, Joe, and Tammy stop the fighting between Zoroark and the guardian protectors.
Ash carries an injured Celebi to the Time Ripple at the stadium, followed by Kodai. Kodai’s Mismagius traps Ash and Celebi with telepathy, and his Shuppet injures Zoroark, preventing them from reaching the Time Ripple. Kodai believes he has absorbed part of the Time Ripple and replenished his power, confessing that he has fooled the townsfolk twice with his media manipulations. However, Zoroark soon reveals Kodai’s victory is an illusion created by Zoroark. Kodai tries to reach the Time Ripple but is blocked by the guardian protectors, and Zoroark traps him in the stadium by using its remaining strength to make an illusion of Kodai’s ship.
Zoroark collapses from its injuries. Celebi ventures into the Time Ripple to rejuvenate its own power and revive Zoroark, before departing back to the future. Kodai’s confessions are played on television news, and he is promptly arrested. Zorua and Zoroark depart for their home region.