Ash, Pikachu, and company stop by in a house where they intend to watch a match of the Pokémon Baccer World Cup between the evolutionary line of Elekid and Beldum. Brock explains about what the Pokémon Baccer World Cup is, and an image of a mysterious man shows up after the match in the TV and exhibits its team formed by a Raikou, Entei, and Suicune, that quickly drags the spinning-top shaped object in the floating pyramid, making the gang want to see them live. Recognizing them as legendary Pokémon, Team Rocket starts getting excited that they should capture them. A Nurse Joy then shows up, saying that she is also very excited for the match. Ash then proposes to reach Crown City before the day's end, where the next Pokémon Baccer World Cup will be held.
Meanwhile, a Zoroark rests in a large carrier plane, and Zorua tumbles out of Zoroark's hair, who seems to be the child of Zoroark. Suddenly, an automatic door opens, where Zoroark and her son find themselves face-to-face with Raikou, Entei and Suicune. Behind them, the business man Grings Kodai and his assistant, Rowena, stay in a chamber. Rowena tells Kodai that the final adjustments are ready. Kodai then tests Zoroark's use of illusions by commanding the illusions of the legendary Pokémon to attack Zoroark. Zorua tries to attack Raikou, but Zoroark stops him and puts him into her hair for safety. Kodai asks Zoroark if she cherishes her son that much, but Zoroark quickly transforms into Raikou. Zoroark fills the area with thunderclouds that ascend to Kodai and Rowena. At the same time, Kodai activates an illusion in his bracelet. The thunderclouds penetrate them, but Kodai reveals that he and Rowena are illusions, and that the cameras were also fooled by the illusions.
Kodai's bodyguard, Goone, soon announced that they will be arriving in Crown City soon. Kodai dismisses the illusions of the legendary Pokémon, and Zoroark transforms back to her own form. After such, Zorua jumps from his mother's head and foresights the zone. Kodai says that the test is over and that Zoroark did a marvelous performance. He sends out a Ninjask, and it captures Zorua, paralyzing Zoroark in place to prevent her from saving him. After Zorua has been taken away, Zoroark immediately rams the ceiling, trying to go after the Ninjask, but fails. Kodai threatens Zoroark, that if she wants her son back, she will need to stay obedient, to which Zoroark roars at him in response.
Unknown to Zoroark, Zorua managed to escape from his Pokémon captors consisting of Scizor and Ninjask, and falls out of the carrier ship. During the fall, he finds a group of Hoppip, Skiploom, and Jumpluff. After a while, Zorua falls off, but quickly transforms into a Skiploom to float safely towards the ground. Inside the plane, Goone confirms to Kodai that Zorua has escaped, but this hasn't changed Kodai's plans, since Zoroark is unaware of Zorua's escape.
Elsewhere, Zorua angers a group of Vigoroth after falling on top of one. Ash and his friends arrive and call out their Pokémon to stop the fighting. The Vigoroth soon lose interest and run off. Zorua claims that he didn't need any help, to which Ash, Dawn, and Brock argue with him until they all realize that Zorua is talking to them through telepathy. Zorua then says that he is going to Crown City where his Mom, Zoroark, is. Ash and his friends agree to help him, and Zorua shows off his ability by transforming into Ash. After Kodai blackmails Zoroark, by using an illusion image of Zorua, Zoroark began destroying Crown City in the guises of Raikou, Suicune, and Entei. Kodai simultaneously frames Zoroark for this by airing a public message in order to have the town all to himself.
The real Suicune (in shiny coloring) calls upon the other two of the trio. Celebi, returning to the town for the first time in twenty years, is presented with its own crisis, due to that prior to the movie, businessman Grings Kodai discovered Celebi in Crown City, and touched the "ripple of time" that was produced due to Celebi's time traveling. As a result of this, Kodai gained the ability to have powerful visions that show him the future, while destroying all of the greenery within the city unbeknown to its citizens. The gang meets up with Karl, an investigator, currently researching Grings Kodai. He tells them about Grings, nicknaming him "The man who can see the future". During this, Kodai has a vision in which he sees Ash, Dawn, Brock, Karl, and Rowena try to stop him from touching the ripple. Zoroark had escaped her kidnappers, but Goone later recaptures her.
The gang later discovers that Kodai manipulated the footage shown to the citizens as part of his plan. Kodai later goes around town trying to find the countdown clock with the "ripple" which he saw in his previous vision. Discovering that Ash is in the city, Kodai has Goone send out the Pokémon to find and capture him. Zorua, followed by Pikachu and Piplup, runs away to look for its mother. While they're meeting and playing with Celebi, the gang's been captured by Kodai. Meanwhile Rowena is looking through Kodai's archives discovering myths and old stories regarding the town and Celebi. She then reveals herself to the gang while telling them everything she discovered. She tells them how 20 years ago he not only tampered with the ripple gaining his visions but he attacked Celebi reversing the flow killing the greenery. His power, however, is rapidly leaving him.
While Celebi plays in the tree, one of Kodai's machines discovers it. Soon, the Pokémon begins to fight against him. Before fainting, Zorua sends one final message to his mom before fainting. This message sends her on a berserk rampage, destroying everything in her path. While on the plane, she is confronted by the three legendary Pokémon. Kodai violently attacks Celebi forcing it to call upon the ripple early. Zorua quickly regains consciousness and fights Kodai. Elsewhere, a conflict between Zoroark and the legendary Pokémon has begun to get out of hand, destroying Kodai's plane.
Later, Celebi and Zorua are saved by the gang who counter attacks then rapidly flees. The battle between Zoroark and the legendary Pokémon continues as Zoroark proves to be too much. Meanwhile, the gang goes to Karl's grandfather's workshop. They learn that Zoroark and the legendary Pokémon are fighting in town. They discover one final clock near the stadium where the "ripple" will appear. They also learn that Kodai has learned of this by using his spy technology. As a race to the stadium progresses Zoroark has used its illusion to prevent the legendary Pokémon from further attacking. As the Pokémon prepare to finish it off, all the city's Pokémon circle around Zoroark protecting it.
Brock, Dawn, and Goone have a battle while Ash and Kodai also battle near the stadium. During Goone's battle, Zoroark comes out of nowhere and attacks all of his Pokémon hurting both him and the Pokémon. Soon, Celebi finds itself and Zorua chased by Kodai's minions. The pursuit forces them into the Pokémon Baccer Stadium, where they are cornered by Kodai, who captures Zorua in order to blackmail Zoroark once more. Kodai then finds what he believes to be the ripple of time, and begins to absorb its power. The "ripple of time" ends up actually being an illusion created by Zoroark, who attacks Kodai but is promptly defeated by the angry man. Everyone soon confronts Kodai. The beasts prevent him from touching the rift. While running away, Zoroark traps Kodai in an illusion of him on top his plane high in the air which quickly goes away causing him to fall off the Platform. Zoroark's injuries soon become too painful for her to continue causing her to collapse. Zorua then creates an illusion around them of the two's home. Celebi then uses the power of the true ripple of time to heal Zoroark, then leaves. As Kodai regains consciousness he sees that the entire town is seeing everything that has occurred and all he said. Goone and Kodai are subsequently arrested. In the end, Karl and Rowena take the Zoroark and its child back to Unova. During the credits, Goone and Kodai are seen in a prison.