Zoroark and her adopted child Zorua were abducted in Unova by the film's antagonist, businessman Grings Kodai. After seeing Zoroark's skill in illusions, Kodai threatened Zorua's safety in order to blackmail Zoroark into attacking Crown City under the guises of Raikou, Entei, and Suicune. Though Zorua was able to escape from Kodai's ship, Zoroark was unaware of the fact and continued to attack the city in exchange for Zorua's safety. She begins destroying the surrounding city in illusions of its destruction, transforming into the legendary beasts one by one: causing floods as Suicune, walls of fire as Entei, and destroying priceless statues as Raikou. While this happened, Kodai edited the videos that recorded Zoroark attacking the area, making it seem that Zoroark was actually destroying Crown City instead of making illusions of its destruction. Once the task was done, Zoroark was imprisoned once again and taken back to Kodai's airship, having been lured into a trap by a projection image of Zorua made by Goone. She is seen trying and failing to break free of the cage inside the ship.
Hearing Zorua's cry for help, Zoroark found the strength and motivation to break free of her prison and began making her way to where Zorua is. However, the three legendary beasts that serve as guardians of Crown City saw Zoroark as a threat, believing her to be the cause of the city's destruction, and attacked her. Zoroark's battle with the three beasts made its way through the town, with Zoroark trying to drive them off long enough for her to get to Zorua. When the legendary beasts corners Zoroark once again, Zoroark used an illusion to trap the legendary beasts in thorn-covered vines in retaliation, but Rowena breaks the illusion and frees them. The wild Pokémon who took shelter came to the legendary beasts, trying to explain to them that Zoroark isn't the enemy. Zoroark is confused, but stops attacking as well.
With the misunderstanding settled, Zoroark continues making her way towards the stadium, defeating Goone and his Pokémon along the way in a vengeful fury. Zoroark finally reaches the Pokémon Baccer World Cup Stadium, intent on saving her child and taking her revenge on Kodai. Before she can reach him, Kodai reveals he has recaptured Zorua and threatens to kill the child, electrocuting Zorua to prove his point. Seeing this, Zoroark has no choice but to stop and allow herself to be brutally assaulted by Kodai's Shuppet. However, when it seemed that Kodai finally absorbed the power of the Ripple of Time, Zoroark smirks as he's horrified to find it was all an illusion she created. Zoroark's deception allowed Karl to catch Kodai gloating about his actions to Ash on camera.
With Kodai's plan seemingly ruined, Zoroark is finally able to move in to reunite with Zorua, who tries shakily to reach his mother in return. However, their reunion is soon interrupted by Kodai, who sent his Shuppet to attack Zorua with Shadow Ball only for Zoroark dive into its path and take the attack to protect her son. Before she can recover from the attack, the enraged Kodai attacks and mortally injures Zoroark by electrocuting her, but she manages to counterattack with Dark Pulse, destroying Kodai's time ripple absorbing claw and defeating his Shuppet while Ash and Dawn manage to defeat his Mismagius. The tables now turned, Zoroark moves in on the now defenseless Kodai, only for him to make a run for the ripple of time and be cut off by the arrival of the legendary beasts, sending Kodai running for his life. However, Zoroark suddenly collapses from the wounds sustained in the fight, having taken too much damage to continue. In a final act of revenge on the man who'd kidnapped her child, Zoroark uses her Illusion Ability on Kodai one last time, who was seeking shelter at the World Cup Stadium, making him believe he has escaped to the safety of his airship, only for her to cancel out the illusion and send Kodai falling from a high balcony to the field below, knocking him out cold. Zoroark lets out a satisfied smile after finally avenging the suffering that Kodai caused her and her child, and closes her eyes.
Zorua cries out for his mother and attempted to wake her, but with no success, and everyone fears the worst. After regaining its strength with the use of the real ripple of time, Celebi uses the energy field in order to revive Zoroark. Zoroark awakens, then embraces her beloved son, finally reunited. Alongside the main protagonists and her son, Zoroark then corners Kodai as he awakens, the tape of him gloating about his past actions that devastated Crown City twenty years ago being broadcast live to the entire town. Exposed, Kodai is arrested for his crimes and Zoroark lets out one last roar, justice having finally been done. The next morning, Zorua and Zoroark are boarded on a ship heading back to Unova with Karl and Rowena. Before they departed, Zoroark took on the form of Pikachu and she returned to her original form when Zorua had taken on the form of Ash, playing along with his trick.
In the credits, Zoroark and Zorua were last seen nuzzling each other affectionately when the ship approaches a mist-covered island, presumably their homeland.