With Meloetta in their possession, Team Rocket's Giovanni controls Tornadus, Thundurus and Landorus in their more powerful Therian Formes though use of the reveal glass unlocked by Meloetta's presence and Meloetta's song. Ash, Cilan, Iris, Cynthia, and Ridley do their best to free Meloetta and save the world from Team Rocket. But forces stronger than Team Rocket are present, and Giovanni soon finds himself not able to control himself and sets Tornadus, Thundurus, and Landorus on a path to destroy Unova rather than take it over for Team Rocket.
Ash continues to train at Cynthia's villa until Ridley (a member of an ancient civilisation dedicated to protecting Meloetta) and his Golurk hear Meloetta's song and come to take Meloetta back. At first, Ridley assumes Ash is associated with the thieves, but this turns out not to be the case. Before Ridley can take Meloetta home, Team Rocket assaults the group and capture Meloetta and summon up the ancient Abyssal Temple through its power and song. The heroes try to fend off Team Rocket, but with Giovanni himself present they are too strong.
While still staying at Cynthia's villa and training for the Unova League conference, Ash and the gang come across a fighting pair of Rufflet and Vullaby. It turns out they have both escaped the inexperienced Day Care Nurse, Layla. Whilst the manager is away, Ash, Iris and Cilan help Layla in the Nursery, but the ongoing conflict between the two Pokémon both craving Layla's attention continues.
Ash, Iris, and Cilan help Cameron get to Humilau City where he wants to challenge Marlon for his own eighth Unova League Gym Badge. On the way, Ash and Cameron are separated from the group. Ash almost falls off a cliff, but then Cameron saves his life. Cameron has a "great idea" and he gets out what seems to be a "map", which was a table cloth. As they continue heading down a road, it starts to rain and then they take shelter in a nearby cave. Realizing that they didn't have any food, Ash, Cameron and their Pokémon are hungry as Meloetta leaves only to come back with an apple. Meloetta leads them to an apple tree where they harvest the apples to bring them back to the cave to munch on them. After they ate the apples (and Cameron's Riolu hiccups adorably), they decide to stay the night in the cave until the rain stops. Ash and Cameron exchange their goals in life. Ash wanting to a Pokémon Master while Cameron wanting to be the best Pokémon Champion in the world.
The Pokémon World Tournament Junior Cup begins, with rivals such as Trip, Georgia, and Burgundy showing up to take part in the tournament. After an exhibition match between Sinnoh Champion Cynthia's Garchomp and Unova Elite Four member Caitlin's Gothitelle ends in a no official winner, the first round begins. Iris is up first against Georgia, with Iris's newly captured Dragonite being pitted up against Georgia's Beartic.
After learning the Unova League conference will not be held for three more months, Ash, Iris, and Clian meet up with Cynthia, the Sinnoh Region Champion. She says she has come to Unova to participate in an exhibition match at the Pokémon World Tournament Junior Cup, held in Lacunosa Town, and Ash learns that the prize of the tournament is a battle with Alder, Unova's reigning Champion. As the four head out of Virbank City for Undella Town, they come across the legendary Melody Pokémon, Meloetta who seems to have fallen ill.
After Ash and the gang arrive in Virbank City and Cilan gives them a rundown of the area’s history, they run into their filmmaking friend Luke and his Zorua! Thanks to winning a film festival with the movie our heroes helped him make (The Legend of the Pokémon Knight), Luke is there to attend a preview event for Pokéstar Studios, a theme park opening soon within the film studio lots.
The group meets up with Dragon Buster Georgia who has a Vanilluxe now. They travel to the Ferroseed Institute to see the Moss Pokémon Ferroseed being studied, but when an accident forces an evacuation, Iris, her Axew, Ash's Oshawott, and Georgia's Vanilluxe are trapped inside. Iris has not yet overcome her crippling phobia of Ice-Types, and she must figure out a way out with Vanilluxe at her side.
With only one more badge left, the group heads to Opelucid City so Ash can challenge the Gym Leader. Unfortunately for Ash, the Gym in Opelucid City is closed. When the group stops in Stonesthrow Town, Cilan meets little Marigold who is picking out her first Pokémon today. Cilan offers his skills as a Pokémon Connoisseur, but another A-Class Connoisseur named Ricard Nouveau offers up his services instead of Cilan's, and they have a battle to determine who is the better Connoisseur. All while the S-Class Connoisseur Fauxgundy watches, but they believe they have seen her somewhere before.
During a practice match against Iris' Emolga, Ash's Swadloon evolves into Leavanny. Leavanny's leaf-sewing process causes it to make costumes for the other Pokémon, but this causes Axew to be accidentally kidnapped by a pair of Durant who are building a den. They stop to think about how they are going to enter the Durant's den, and to be able to rescue Axew.
After winning his sixth badge, Ash and friends bump into Stephan. He is in town to compete in the Bell of Wishes Festival that is being held that day. Ash, Iris, and Cilan, after finding out that the winner gets to ring the bell atop Mistralton Tower and get a wish granted, decide to compete in the festival.