The story begins that Sonic and his team along with some of their friends are asked to take a S-class mission from an important buisness from Crown City. Tsunade has her doubts about the mission, so she decides to a back-up squad to investigate their client consisting of Shikamaru, Ino, Choji, Gajeel, Kazama, Levy and Elfman.
Meanwhile Ash, Pikachu, and company stop by in a Pokémon Center where they intend to watch a match of the Pokémon Baccer World Cup between the evolutionary line of Elekid and Beldum. During the match, Team Rocket disguise themselves as janitors and ask Ash and co. what they're watching. Brock explains to them what the Pokémon Baccer World Cup is, and an image of a mysterious man shows up after the match on 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 to get excited about capturing them. A Nurse Joy then shows up, saying that she is also very excited for the match. As usual, Brock fell in love with Nurse Joy, and Croagunk attacked him, then pulled him away. Ash then proposes to reach Crown City before the day's end, where the next Pokémon Baccer World Cup will be held. Brock quickly recovers and says that he will lead Ash and Dawn through shortcuts.
Meanwhile, a Zoroark rests in a large carrier plane, and Zorua fumbles out of her fur, who seems to be Zoroark's child. 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, observing the two Pokémon. Kodai then tests Zoroark's use of illusions by commanding the projections of the legendary beasts to attack Zoroark. Zoroark quickly transforms into Raikou and fills the area with thunderclouds that ascend towards Kodai and Rowena. At the same time, Kodai activates an illusion in his bracelet. The thunderclouds penetrate them, but Kodai reveals that Rowena and himself are illusions, even the cameras were fooled by the illusions.
Kodai's bodyguard, Goone, soon announced that they would be arriving in Crown City soon. Kodai dismisses the illusions of the legendary beasts, and Zoroark transforms back to her true form. After such, Zorua jumps from his mother's fur 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. Kodai controls Zoroark by threatening to harm Zorua, whom she cares for like if he were her own child. Zoroark then angrily roars at Kodai in response. Unknown to Zoroark, Zorua managed to escape from his Pokémon captors consisting of Goone's Scizor and multiple Ninjask, and falls out of the carrier ship. During the fall, he finds a group of Hoppip, Skiploom and Jumpluff, grabbing one of the Skiploom's bloom and transforming into one to float safely towards the ground.
Inside the plane, Goone confirms to Kodai that Zorua has escaped, but it hasn't changed Kodai's plans, since Zoroark is unaware of Zorua's escape. Meanwhile, Zorua angers a group of Vigoroth after falling on top of one, and Ash and his friends arrives and calls 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 Meema, Zoroark, is headed. Ash and his friends agree to help him, and Zorua shows off his ability by transforming into Ash then Pikachu.
Sonic and Naruto and team come to Kodai's office to hear what is their mission since Tsunade didn't have the proper information for the mission that Kodai paid for. He tells them that their mission was to keep an eye out of the evil Pokemon called Zoroark. While Kodai informs Team Sonic, The invetigation squad decides to do some investigating on Kodai's background and what is his true plan. During this, Shikamaru and Kazama find out that Rowena is a spy and her job is to investigate Kodai as well.
Afterward Kodai blackmails Zoroark by using an illusion image of Zorua, Zoroark began destroying Crown City under the guises of Raikou, Suicune, and Entei in illusions of the city's destruction. At the same time, Kodai frames Zoroark as an evil Pokémon by airing a public message and showing edited footage of the town actually being attacked in order to have the town all to himself. While this happens, the real Suicune, Entei, and Raikou, who serve as the guardians of Crown City, sensed that the city was in danger and began making their way to the town to defend it.
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 the time that Zoroark goes on a rampage, Sonic, Naruto, Natsu and Gajeel run into Ash, Dawn, Brock, Pikachu and Zorua on the other side of the bridge after they have a little race out of town only to get in trouble with Sakura. After Zorua transforms intoBrock, Our heroes chase after him and met Karl who manages to let them into the Crown City.
Meanwhile, Kodai has a vision in which he sees Ash, Dawn, Brock, Karl, and Rowena along with Sonic and his friends trying to stop him from touching the ripple. After Zoroark had escaped her kidnappers, but Goone later recaptures her by using a projection of Zorua. The gang later discovers that Kodai manipulated the footage of Zoroark attacking the city using her illusions shown to the citizens as part of his plan. Before they go any farther, Sakura attacks Sonic and Naruto for not informing them about their race. 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 his Pokémon to find and capture him.
Zorua runs off to find Zoroark on its own, but is stopped by Joe's Mightyena and lulled to sleep by Tammy's Tangrowth. Ash and the gang catch up to Zorua, and Karl is met up with his grandfather, Joe. Hearing Zoroark trying to escape her prison on Kodai's ship, Zorua awakens and resumes his desperate search for its mother, followed by Pikachu, Lucario and Piplup. However, they find themselves surrounded by a group of angry Pokémon, who were angry at Zorua for what Zoroark did to the city. Before a fight broke out, Celebi appears and calms things down by making the greenery around them bloom into berries. Zorua befriends Celebi when it agrees on help Zorua find its mother, and they resume their search. Shortly afterward, Ash, Dawn, Brock, and Karl have 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 twenty years ago, Kodai not only tampered with the ripple, which in the process gained his visions but he attacked Celebi, reversing the time flow and killing the greenery. His power, however, is rapidly leaving him.
While Celebi, Zorua, Pikachu, Lucario and Piplup were still on their search for Zoroark, Kodai finds Celebi with Zorua and he attacks Celebi. Zorua fights Kodai and his Pokémon using illusions to protect Celebi, but is knocked back. Before fainting, Zorua sends one final message to his mother. This message gives Zoroark the strength to break free of her prison and began making her way to where Zorua is. While on the plane, she is confronted by the real Suicune, Entei, and Raikou, who are convinced that Zoroark is an enemy for destroying the city. Kodai violently attacks Celebi forcing it to call upon the ripple early. Zorua quickly regains consciousness and fights Kodai again, but proves to be no match for him. Fortunately, the arrival of Ash, Sonic and their friends counter attacks Kodai in a heated battle, saving Celebi and Zorua before rapidly fleeing to safety.
Elsewhere, a conflict between Zoroark and the three legendary Pokémon has begun to get out of hand, destroying Kodai's plane in the process. The battle continues through the town of Crown City as Zoroark proves to be too much. She manages to blasts Suicune, Raikou, and Entei for a short while using her Night Daze attack before resuming her search for Zorua.
Meanwhile, the gang goes to Joe's workshop. They learn that the guardians of Crown City, Suicune, Entei, and Raikou are attacking Zoroark and are fighting her through town. They also 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 finds herself surrounded by the legendary beasts again, and uses her illusions to trap them in crystallized thorns in order to prevent the legendary Pokémon from attacking further. Zoroark's illusions were quickly broken by Rowena's illusion canceler, and the legendary beasts are freed but were still ready to attack Zoroark. However, the Pokémon who live in the City appeared and quickly stood between the guardians of Crown City and Zoroark, trying to explain to Suicune, Raikou, and Entei that Zoroark isn't the enemy. Zoroark is confused at this, but stops attacking as well.
Brock and Dawn along the rest of Team Sonic and the others have a battle with Goone to buy Ash, Sonic, Naruto, and Kurama enough time to get to the ripple of time. During Goone's battle, Zoroark comes out of nowhere and attacks all of his Pokémon in a vengeful fury, knocking him and all his Pokémon out with ease. Kodai manages to catch up to Ash and Celebi makes a run for it, only to be hunted down by Kodai. However, the 'Celebi' is revealed to be Zorua flying with aid of Karl's Bronzor. Both try their best to take Kodai down but his Pokémon quickly knock out Bronzor and Kodai uses the claw he intends to use to absorb the ripple in time to capture Zorua.
At the Pokémon Baccer Stadium, Ash lets the real Celebi out of his backpack and they try to reach the ripple in time. However, Kodai arrives and corners Ash, Sonic, Naruto, Kurama, Pikachu, and Celebi, then begins making his way to the ripple of time. Zoroark appears and charges at Kodai to take her revenge and reclaim her child, but the businessman forces Zoroark to stand down by threatening to kill the captured Zorua if she interferes, proving his point by electrocuting the young Pokémon in front of her. Kodai cruelly orders his Shuppet to finish off Zoroark as he approaches the ripple of time and begins absorbing its power, not caring if the city's greenery will wither and die again. As the events that happened 20 years ago start to repeat themselves, Kodai gloats over his apparent victory to Ash, but Zoroark suddenly smirks, and time reverses itself. The "ripple of time" Kodai absorbed was actually an illusion created by Zoroark to deceive him, allowing Karl and Rowena to capture Kodai's revelation of him being responsible for Crown City's disaster on video. Wondering how come the illusion affected him, Kodai finds that Zorua destroyed his illusion canceler when he attacked him previously. While Kodai is distracted, Zorua manages to recover and desperately tries to reach his mother to reunite, but Kodai, furious at the deception, orders his Shuppet to attack Zorua from behind, only for Zoroark to take the attack to save her son. Before she can recover, Kodai cruelly attacks Zoroark with his claw, electrocuting and mortally wounding her. Zoroark manages to fight through the electrocution, attacking Kodai and defeating his Shuppet, destroying his claw in the process. Kodai, now desperate for the real ripple of time, makes a run for it but is stopped and scared away by Suicune, Entei, and Raikou, now knowing the true threat to the city. Afterward, Zoroark's injuries soon become too painful for her to continue, causing her to collapse.
While Kodai was running away, Kurama traps him in an illusion/ genjutsu to deceive him that he was safe atop his plane high in the air. He quickly cancels the illusions out, causing Kodai to fall off the platform he was on and passes out in the stadium field. Zoroark then closes her eyes with a satisfied smile, glad she was glad that a fellow demon fox able to defeat Kodai. In tears, Zorua pleads and cries for Zoroark to wake up, then creates an illusion of a beautiful grassy field around them, their home. Celebi then uses the power of the true ripple of time to heal itself and heal Zoroark. As Zoroark recovers, she and Zorua embrace in a tearful reunion, and Zorua thanking Celebi for saving his mother. Celebi smiles and then time travels away in billows of light after making the area's greenery bloom.
As Kodai regains consciousness, he awakes to witness all he said while absorbing the false ripple of time being broadcast all over the news and finding himself surrounded by the entire town, Zorua, and Zoroark. Officer Jenny, now seeing his true nature, arrests Kodai for his crimes as Zoroark and Kurama (In a Henge clone) roars at him, glad to see him brought to justice. Afterward, Zoroark and Zorua board on a ship heading back to Unova with Karl and Rowena. Before they departed, Zorua mischievously took on the form of Ash and is instantly turned back to his original form when Rowena touches his tail, while Zoroark took on the form of Sonic before transforming back to her true form after her son is revealed. As the ship sails, Ash and Sonic yells out a promise to Zorua that he will come to Zorua and Zoroark's homeland one day.
- Guest Starring: Shikamaru, Ino, Choji, Gajeel, Kazama, Levy and Elfman (The Investigation squad) Wendy, Drake, Hinata, Kikiyo Uzumaki (Naruto's Cousin)
- Kurama is somewhat related to Zorua and Zoroark
- Naruto lets out his secret about Kurama and thet he use his clone to allow Kurama to communicate with Naruto physically
- Naruto shows off a new technique that allows Kurama to have a physical form without harming Naruto
- In The epilouge, Moewth from Team Rocket decides to quit because he's tired from all the trouble they get into from either going after Pikachu or Pooh Bear (Pooh Adventure Series Reference). So he leaves Jessie and James to join Sonic and friends
- Nancy, June, Thomas, Molly, Oscar and Annie are mention 6 times.