While Ash is doing some special training at Cynthia’s house in preparation for the Unova League, the villains of Team Rocket are finishing preparations to launch their latest diabolical scheme: Operation Tempest!
After watching a training battle, Meloetta wants in on the action. Ash and Krookodile have just accepted Meloetta’s challenge when an enormous Golurk descends upon the battlefield, ridden by its Trainer, Larry—who immediately accuses Ash of being a villain and kidnapping Meloetta! The misunderstanding is quickly sorted out, and Larry explains that he’s one of Meloetta’s protectors, and that he and Golurk have been looking for the Mythical Pokémon for quite some time after it was taken away by some unknown villains.
The villains in question quickly make themselves known: a pair of Team Rocket agents have tracked Meloetta to Cynthia’s house, intending to recapture it! Larry says he and Golurk will battle them while Ash and the others get Meloetta out of harm’s way. The group begins their run—but their path is soon blocked by Jessie, James, and Meowth! Iris and Cilan stand against them while Ash, Pikachu, and Meloetta go on alone.
Unfortunately, they’re playing right into Team Rocket’s hands, and the Boss is waiting to apprehend them! Giovanni and his Persian trap Ash and Pikachu in a cage, and he orders Meloetta to surrender or watch its friends be hurt. Meloetta has no choice, and the three of them are taken onto Team Rocket’s helicopter, then transferred into a submarine that descends to a ruined temple at the bottom of Undella Bay.
Ash watches helplessly as Meloetta is restrained inside the temple. Dr. Zager begins to play a recording of Meloetta’s haunting song, which unlocks an ancient seal, transforming the temple and raising it to the surface of the bay. As soon as the path is clear, Giovanni makes his way to the innermost part of the temple and claims the Reveal Glass—a mystical mirror with unknown powers! What is Operation Tempest really about? Could this be the greatest threat the Unova region has ever faced?!
Somewhere in the sea near Unova a Team Rocket helicopter lands on a floating platform. Giovanni comes out of the helicopter along with a few Team Rocket Grunts and is welcomed by Jessie, James, Meowth and Dr. Zager. Team Rocket's plan involving Meloetta will finally commence.
Meanwhile, at Cynthia's villa in Undella Town, Ash and Cilan have a training battle, with Ash's Oshawott battling with Cilan's Pansage. Cilan commands Pansage to use Bullet Seed, but Ash orders Oshawott to use Razor Shell. Meloetta likes their battle and transforms in its Pirouette Forme, wanting to battle too, against Oshawott. Oshawott doesn't want this, as he is in love with Meloetta. Ash, who thinks a battle against Meloetta would be cool then sends out Krookodile and the two start their battle. Meloetta uses Hyper Voice, but Krookodile manages to hold on. Ash orders him to use Stone Edge, but Meloetta manages to take all stones with its fighting techniques. Ash then orders Krookodile to use Dragon Claw. However, before he hits Meloetta, a Flash Cannon comes out of nowhere, which is revealed to come from a Golurk. The Golurk flies down and lands and a mysterious man appears to its side. He falsely thinks Ash and his group are villains for attacking Meloetta and tells the Golurk to attack them, but Meloetta steps in between and the man understands that they are Meloetta's friends.
The man introduces himself as Ridley. He explains that he and Meloetta lived a peaceful life in their village, until Team Rocket came in and stole Meloetta. He tried to stop them, but Team Rocket managed to escape with Dr. Zager's helicopter. Ridley then explains that Team Rocket kidnapped Meloetta to use its ability to summon the Abyssal Ruins.
Their conversation is short-lived as Team Rocket surrounds Cynthia's villa and creates a dark fog. Ridley and Meloetta try to escape but they are stopped by a Golem and a Rhydon used by two Team Rocket Grunts. The Rhydon uses Megahorn but Ridley shields it by ordering his Golurk to use Heavy Slam. Golem then uses Rock Blast. Ridley orders Ash his friends to escape while he battles them. After that, Ridley has Golurk to use Heavy Slam again to take out Rhydon. Golem uses Steamroller to attack.
Ash and his friends continue to run away from Team Rocket, but are now confronted by Jessie, James and Meowth. James has his Yamask to use Will-O-Wisp to trap them. Meloetta tries to escape by turning invisible, but James uses his infrared glasses and orders Yamask to use Shadow Ball. Ash and Pikachu run away while Cilan and Iris stay behind to battle.
Pikachu suddenly stops, sensing another Pokémon. This Pokémon turns out to be none other than Giovanni's Persian, which Ash's scans with his Pokédex. Giovanni appears as well, having come to steal Meloetta. He orders Persian to use Shadow Claw, but Ash orders Pikachu to use Iron Tail to take him down. Giovanni, upon seeing Meloetta has turned invisible with his infrared glasses, orders his Persian to use Power Gem to take Ash and Pikachu down. This also causes Meloetta to appear, in shock. A helicopter traps Ash and Pikachu with a synthetic cube. Giovanni orders Meloetta to come with him or else he will crush Ash. With no other options, Meloetta agrees and comes with him. The cube containing Ash and Pikachu is also taken along. They head to the Abyssal Ruins where the final stage of Team Rocket's plan begins.