After defeating his latest opponent in a Pokémon battle, Ash and co. rush to the nearest Pokémon Center. Once there, they watch the Pokémon Backer match on television. They cheer loudly as Rioka's Elekid struggles to make a goal and succeeds, slowly closing the gap between her and her opponent. Team Rocket, disguised as janitors working at the Pokémon Center, asks the gang what they're doing and Ash explains Pokémon Backer to them. Just then, Kodai appears on the television screen advertising the "Pokémon Backer World Cup" which is to be held in Crown City in just a few short days. The monitor shows an Entei, Raikou, and Suicune playing a game of Pokémon Backer and easily scoring a goal. Ash, Dawn and Brock think that it would be awesome to see and make Crown City their next destination, while Team Rocket hatches a scheme to steal the three dogs for themselves.

Meanwhile, flying in the heart of the night sky is a large carrier plane. Inside sleeps Zoroark, while Zorua stirs and fumbles out of Zoroark's long red hair. A steel door opens and the three legendary dogs approach the Pokémon. Watching from a skybox, Kodai urges Zoroark to show him what it can do. Zoroark quickly tucks Zorua into its hair and creates a black cloud around them. While Kodai's assistant freaks out, Kodai uses a device on his wrist to break the illusion and proves that they're fine. After transforming into one of the dogs and then back into itself, Kodai seems satisfied. Zorua emerges from Zoroark's hair, wanting to fight too, but a Ninjask appears and abducts it. Zoroark goes into a rage, but Kodai shocks it and explains that Zorua will be safe so long as Zoroark does whatever he says. Kodai closes the door on Zoroark, and the three dogs, which turn out to be illusions created by Kodai, disappear and the ball-like devices that created them sink into the ground. Zorua manages to slip from Ninjask's grasp and escapes through a hatch in the wall. It is quickly confronted by a Scizzor, but Zorua transforms into Scizzor and starts laughing, confusing the Pokémon. Zorua continues to makes its escape and plunges through another hatch, arriving on the outside of the airship. Zorua loses its grip and plummets to the ground below. Thankfully for Zorua, it manages to land on top of a Skiploom's head, allowing it transform into one and slowly and safely descend toward the ground. Kodai is informed that Zorua has escaped, but he mentions that it's not a problem so long as Zoroark thinks they still have Zorua held captive. As his carrier ship approaches Crown City, he can't help but feel anxious. At that moment, Celebi appears from a time rift.

The title sequence plays.

Team Rocket is seen pedaling a balloon after Ash, Dawn, and Brock, but Zorua lands on them and forces them to make a crash landing. Zorua then lands on top of a Vigoroth, and it is not happy to be disturbed. Zorua transforms into one, but the Vigoroth is not amused and soon Zorua is forced into a corner against a cliff's edge by a large group of them. While Ash and Dawn pester Brock about being lost, Pikachu's ears pick up the sound of Zorua in distress and the gang looks over to find Zorua surrounded. Despite how grim the situation looks, Zorua is still laughing. Ash sends out Infernape and Dawn sends out Mamoswime, ordering the mass of Vigoroth to leave Zorua alone. Piplup tries to stand tall and join in, but trips and slams into a tree. Piplup stands again and begins shouting at the Vigoroth. Not in the mood for a fight, the Vigoroth all leave. Zorua thanks them, but claims it could've defeated them without their help. Ash, Dawn, and Brock argue with Zorua before suddenly coming to the realization that it's using telepathy to talk to them. The group spots Crown City from the cliff and Zorua announces that the city is evil.

As Ash and company follow Zorua to Crown City, Zorua explains how it was separated from its mother, and they agree to help it find her. Zorua shows off its ability to transform by turning into Ash. The group looks on in shock while Zorua grins evilly and hops away, telling them to follow. They spot Zorua's tail sticking out and Pikachu grabs onto it, reverting Zorua into its true form. Zorua laughs and then transforms into Pikachu, hitching a ride on Ash's shoulder. Kodai's ship makes its way toward the city and Kodai orders for Zoroark to cause havoc, using a video of Zorua trapped in a cell as insurance. Zoroark growls and heads out to the town.

In Crown City, Celebi begins greeting all of the Pokémon. A girl named Proof gets ready to cheer for her favorite team at the "Pokémon Backer World Cup" and greets an elderly woman along the way. As she leaves, the woman spots Celebi and her flowers start to bloom. She runs off to meet with an elderly man and cheers that Celebi has returned, bringing tears of joy to their eyes. Zoroark appears in the town and recalls Kodai's words to her. She begins destroying the surrounding and transforms into the legendary dogs one-by-one: causing floods as Suicune, walls of fire as Entei, and destroying priceless statues as Raikou. Everyone runs in horror and they are all forced to evacuate the center area of the city. Back in the plane, Kodai has a vision of Celebi and a countdown clock reading "0000", and then of 5 people appearing to thwart his plans: Ash, Dawn, Brock and two unknown others. Kodai's assistant is concerned, but his male assistant holds her back. Elsewhere, the real three legendary dogs sense something bad happening and rush to Crown City.

Ash and the others arrive at Crown City and are shocked to discover that the city is being ransacked by the three legendary dogs. When they ask Officer Jenny if it's true, Proof appears and explains that she was nearly swept away in a flood created by Suicune. When they ask if it'll affect the World Cup, Officer Jenny assures them that it will still happen. A message on a television screens alerts the townspeople that the town is actually being attacked by Zoroark, and he will do his best to stop it. Zorua begins crying out for his mother and transforms into Brock, running away in an effort to locate her. Ash, Dawn and Brock chase after him, asking him if his mother would really do such terrible things, but another man has also been made curious. The man is revealed to be Kuruto, and after noticing two Brocks, finds out about Zorua. Kuruto reveals another way inside the center portion of the town through the sewer system and uses a Bronzor to lead the way. Kuruto explains how Kodai is a man of wealth of power, and how he virtually controls all of the media in the media in the world.

Celebi spots Zoroark and hides, fearing for its life. Zoroark then spots Zorua running up to it and happily seeks to reunite. However, Zoroark becomes trapped in an electric cage and Kodai's male assistant takes it away after it's revealed that Zorua was just an illusion. Team Rocket pokes out from behind a tree, cursing the man for stealing Zoroark from them. As the car drives away, Ash and company emerge from the sewers and Zorua immediately searches for his mom, searching around for her. Ash notices a statue of Celebi and Kuruto explains how in the past, Crown City was struck by a strange black magic that destroyed the town, but Celebi appeared and made everything better. Zorua begins sniffing the ground for clues about his mother and Pikachu does the same. In a humorous manner, Ash gets down all fours and sniffs the ground as well. Zorua smirks and transforms into Dawn to mimic Ash, but Dawn isn't amused and grabs his tail, returning him to his original state. Zorua hops onto Ash's head and calls out for his mom, but gets no response. Ash comforts the disheartened Zorua by telling him they'll find her. Kuruto notices that one of the statues destroyed by Zoroark on the television broadcasts has been completely untouched, as well as a bus stop that was also undamaged. Zorua runs off searching for Zoroark, while a camera spots Ash running after him. Kodai is reminded of his vision and orders for Ash to be captured. While searching for Zoroark, Zorua spots a television monitor with Kodai's face and destroys it. Zorua is confronted by an angry Mightyena. As Zorua prepares to fight it, a Tangrowth sneaks up on it and puts it to sleep. The group arrives on the scene and the Mightyena tackles Kuruto, licking him happily.

The elderly man and woman from before emerge and explain what happened when they saw the wall of flame that Zoroark created as Entei. They too explain about what happened in the past and how Celebi saved the town. Zorua finally awakens, confused about its whereabouts, and runs off searching for Zoroark again. When Ash and the others can't follow it through a fence, Pikachu and Piplup are asked to follow it. Zorua runs through the park and becomes surrounded by a group of angry Pokémon. The Pokémon are furious at Zorua for what Zoroark did, and not even Pikachu and Piplup can convince them to stop. Just as it seems like a battle will break out, Celebi appears and calms things down. Zorua transforms into Celebi and Celebi becomes shocked, then excited. Celebi tries to lead Zorua, Pikachu, and Piplup away from the park. Ash and the others follow, but become trapped in an electric cage like Zoroark by Kodai's henchman. Kodai greets them and has them carried away to the airship, where Zoroark has been trying and failing to break free.

Elsewhere, Celebi has taken the Pokémon to the tallest tree in the region, allowing Zorua a chance to try and call out for its mom again. It does, but to no avail. Zorua becomes disheartened by this, but Celebi creates a grassy bed that reminds Zorua of its mother's hair. At the airship, Kodai's assistant has been looking through forbidden files when she receives a call to keep an eye on the cargo that was just carried in. She goes down to find out what's going on and finds Ash and company locked in a cage. She reveals that she's really Rioka, the same girl from the Pokémon Backer match, and releases them. Kodai, meanwhile, has been searching all the countdown clocks in the city for the next energy field and has a vision that he will find Celebi soon. Rioka uses a boat to take everyone away from the airship and informs them about the private data she found in the databases, and what Kodai did in the past.

In the past, Kodai is seen exploring some ancient grounds when he spots Celebi. Celebi attempts to jump into a time field, but Kodai knocked it aside and uses a claw to absorb the energy from it. This gave Kodai the ability to see into the future, but also created a rebound that caused the great disaster in the past.

At the tree, Kodai locates Celebi and Zorua attempts to defend it. Pikachu and Piplup help, but they are knocked away onto a tree branch down below. Zorua is quickly defeated, but Zoroark senses the danger to her child and finds the strength and motivation she needs to break free. She escapes from the airship by making a hole in the roof, but the three legendary dogs appear in the city and arrive at the airship. They seem to be angry about what Zoroark did earlier that day and a battle ensues, with Team Rocket watching from a boat in the harbor. Kodai chokes Celebi and gets the information he needs: the time field is somewhere near a countdown clock with "0000" on it, but he doesn't know where.

As Zoroark battles the three legendary dogs, Zorua awakens and again tries to protect Celebi, with Pikachu and Piplup doing what they can. Everyone arrives at the tree and Kodai realizes that this is exactly what happened in his vision: Ash, Dawn, Brock, Kuruto, and, to his surprise, Rioka have all come to stop him. They manage to rescue Celebi and Zorua thanks to the help of all the Pokémon from the park and flee with their Pokémon, but not before destroying a camera so that they cannot be followed. As they speed away in the boat, Kodai uses a pen that turns turn into a camera to tail them. Meanwhile, Zoroark's battle with Entei, Raikou, and Suicune heads further into the town.

Celebi is taken to the elderly couple's house, where everyone does their best to help heal Celebi's injuries. The elderly couple is more than happy to help Celebi after what it did for them. The elderly man reveals that there is one countdown clock Kodai didn't check after looking at the data Rioka stole; it's the one at the main stadium. Pikachu's ears pick up the sound of something and it destroys the camera. Kodai knows everything. While Zorua is anxious to find its mother, it agrees that helping Celebi comes first. Ash, Dawn, Brock, Pikachu, Zorua, and Celebi set off to find the time rift before Kodai, while Rioka, Kuruto, and the elderly man and woman go after Zoroark.

Zoroark traps the three dogs in an illusion of thorn-covered vines, but then Rioka uses a device on her wrist to break the illusion and free them. Mightyena, Tangrowth, and the Pokémon that had sought shelter with the elderly couple jump in-between Zoroark and the three dogs, trying to explain that she is not the enemy. Zoroark seems confused, but stops her attacks as well.

Kodai spots Ash's group as they attempt to beat him to the stadium, but Dawn and Brock stay behind to try and hold them off. Meanwhile, Ash has made his way through the sewer toward the stadium, with help from Kuruto's Bronzor, and arrives there before Kodai.

Kodai is hot on Ash's trail and attempts to stop him from reaching the countdown clock. Ash throws Celebi into the air and tells it to fly to the time rift before Kodai can get there. Kodai ignores Ash and pursues Celebi, using his Shuppet and Mismagius to defeat it. Celebi turns into Zorua and Kodai becomes angered by the dupe. Zorua attacks Kodai and bites his arm, but Kodai throws him aside. Dawn and Brock struggle to defeat Kodai's goon, but Zoroark dashes onto the scene and quickly defeats him with angry attacks before making her way to the stadium.

Ash takes the real Celebi out of his backpack and slowly makes his way to the time rift. With the countdown clock in sight, they appear to have succeeded, but Mismagius uses Psychic to stop them. Kuruto's Bronzor attempts to protect Ash, Pikachu, and Celebi, but it is defeated with little effort on Kodai's part. Kodai makes his way to the clock, but Zoroark arrives and halts him. Kodai holds up Zorua in his claw and shocks him, threatening to do worse if she does not stand down. Shuppet attacks Zoroark and brings her to her knees. Kodai drops Zorua and makes his way to the time field. He begins drawing power from it, despite protests from Ash, and laughs at the power he receives. As the disaster from the past starts happening all over again and the energy rebounds, Kodai admits what he did in the past and explains that he doesn't care. All hope seems lost!

Zoroark smirks and suddenly time starts reversing itself. It turns out Kodai was nowhere near the energy field and everything was all an illusion. He wonders why the device on his wrist didn't cancel it out and finds that it was broken by Zorua when he bit him. Kuruto emerges from behind a tree and points out that he captured everything on tape. Kodai is finished!

Zorua slowly gets to his feet and makes his way to his mother, who slowly approaches him as well. Zoroark then suddenly jumps over Zorua and takes the brunt of a surprise attack by Kodai's Shuppet. Zorua turns in horror as his mother falls. Kodai angrilly grabs her with his claw and shocks her, but Zoroark manages to break freak and strike Kodai. Dawn and Brock arrive and free Ash, Pikachu and Celebi from Mismagius' attack. Ash tells Pikachu to use Volt Tackle and knocks it out. Zoroark takes out Shuppet. Kodai makes a run for the time energy field but the three dogs block his path. With nowhere else to run, Kodai makes a dart for the stadium. Zoroark finally falls to the ground, no longer possessing the strength to do much else. Zoroark uses her illusion ability one more time to make Kodai think he's arrived safely on his airship before she cancels it out and Kodai falls from a noticeable height to the field below. He falls unconscious and Zoroark closes her eyes with a satisfied smile.

Zorua cries out to Zoroark, begging his mother to awaken. He nudges her and then creates the illusion of a beautiful grass field. He tries to tell his mother that they're home and attempts to wake her with no success. Zoroark isn't moving and everyone fears the worst. Celebi notices the time field and Ash tosses Celebi into it. Celebi disappears for a second and re-emerges good as new. It uses the power from the energy field to revive Zoroark. She opens her eyes and Zorua thanks Celebi for saving his mother. Celebi smiles and time travels after happily making all the flowers in the area bloom, disappearing from sight.

Kodai awakens on the stadium field as a video shot by Kuruto broadcasts to every television in town what Kodai did. He looks to the stands to find everyone, including Officer Jenny, glaring down at him. Officer Jenny tells Kodai that he's under arrest and Zoroark roars at him.

The scene changes to a dock, where Dawn and Brock are seen waving good-bye to Ash, Pikachu, Kuruto, and Rioka as they leave on a boat, presumably to take the two Pokémon home. Ash and Pikachu run up behind Dawn and Brock and wonder why Zorua didn't say good-bye to them. Ash calls out to the Pokémon and Kuruto and Rioka discover that the Ash on the ship has a tail. Pikachu turns into Zoroark and Ash turns into Zorua. Ash runs to the edge of the dock and says farewell. Zorua says "Ash…" to himself and smiles back. The movie ends with Team Rocket floating down a stream.

As the credits roll, Ash, Pikachu, Dawn, Brock and Proof cheer from the stands at the Pokémon Backer World Cup. Kodai and his henchman are being taken away in a police car while the paparazzi photograph them and the news spreads to every newspaper. Entei, Raikou, and Suicune see the boat carrying Zorua and Zoroark off from atop a cliff before returning to their homes. Zoey and her Glameow have taken shelter during a rainstorm. Paul can also be seen exploring some ruins with Palkia and Dialga statues. Ash, Pikachu, Dawn, and Brock make their way to their next destination while Team Rocket follows behind in their balloon. Zorua nuzzles Zoroark affectionately as the two slowly approach a mist-covered island. The final scene has Ash, Dawn, Brock, and all of their Pokémon gazing up at the night sky and watching the sunrise.

Special thanks to Hyper Tails for writing this for us.