Ash and his classmates arrive at Malie City for their two-day exploration. Ash remarks that the city doesn't look very Alolan, and Lillie explains that Malie City was actually modeled on the Johto region. When it becomes windy, Sandy leaps out of Lana's arms and begins circling frantically. It wanders onto the busy road, but Shaymin saves Sandy from an oncoming vehicle. Mallow is pleased by Shaymin's quick thinking and credits the influence of Tsareena, who is busy working with her father at the restaurant. The group arrives at their meeting spot and waits for their guide to arrive. As they do, they encounter a boy clad in ninja garb, posing for several photos for Rotom's travel album. He introduces himself as their tour guide, Charlie Charma, who explains that ninja attire is a Malie City tradition.
Charlie escorts the group to the local Pokémon Center to get changed into more suitable outfits for their day at Malie Garden. At Malie Garden, the students observe the Malie City life from atop the observatory tower. Sandy notices a procession of Eevee pass by, and ends up disturbing it in its eagerness to join in. Charlie announces that he will be leaving for now, and after dropping a smoke bomb, he vanishes into thin air. Everyone then decides to explore on their own. Meanwhile, Team Rocket is trying to sell their new three-in-one Combee doughnuts, but business is rather slow. Jessie looks out of their serving windows and spots the class taking a snack break. She also notices Shaymin, and the sight of the Mythical Pokémon surprises Team Rocket. A sudden gust blows through, taking Mallow's hair ornament, and Shaymin pursues it, followed by Sandy and Meltan. When everyone else notices this, Ash calls out Lycanroc to locate the missing trio. As the classmates begin their search, Team Rocket decides to grab the three missing Pokémon for themselves.
Later, Shaymin spots Mallow's hair ornament on the ground, but the wind picks it up again. The headband then gets stuck on a wooden post, which is too high for Shaymin to reach or climb onto. Lillie and Lana alert Nurse Joy about the missing trio, and she makes an announcement throughout the city. Meanwhile, Meltan and Sandy are also looking for Shaymin and approach the Malie Garden Pokémon for leads, but they haven't seen it. Sandy then picks up a scent and follows it to Shaymin, who had recovered Mallow's hair ornament.
Suddenly, Team Rocket captures the trio in a giant spherical cage and performs their motto. James then explains that the cage is made of a steel alloy that Meltan cannot eat through, but Meltan latches onto one of the bars and dissolves it. The three Pokémon try to flee, but Wobbuffet, Mimikyu, and Mareanie corner them. Shaymin is initially scared, but notices that Meltan and Sandy are keen to fight their way out. Mareanie poisons Sandy with a Sludge Bomb attack, while Meltan fires two Flash Cannons that are dodged. Shaymin calls out in desperation, which alerts Mallow to its location, and she finds them surrounded by Team Rocket. Jessie explains that they are simply trying to steal some Pokémon, before being suddenly knocked to the ground by Lycanroc.
Ash and Lana arrive, and Ash orders Meltan to use Headbutt on Mareanie. She uses Sludge Bomb, but the poison doesn't affect Meltan because of its Steel type, much to the dismay of the Brutal Star Pokémon. Meltan lands a direct hit on Mareanie. Meanwhile, Shaymin uses Aromatherapy to heal Sandy of its poisoning. Lana has Sandy knock Mareanie out with a Double-Edge. Still confident over the chances of victory, Jessie orders Mimikyu to battle, but only after informing it that Pikachu is present. Its Wood Hammer clashes with Pikachu's Iron Tail, so Ash decides to concentrate on the rest of Team Rocket. Suddenly, Stufful walks over to Team Rocket with a Bewear-shaped kite in its paw. As expected, Bewear appears; she straps Team Rocket and their Pokémon to the kite, and also interrupts Mimikyu's match with Pikachu before running off with them. Malie City's extremely strong winds suddenly sweep Bewear off her feet, and send her and Team Rocket flying off into the distance.
Mallow, Ash, and Lana reunite with their respective Pokémon. Shaymin returns the hair ornament, leading Mallow to realize that Shaymin ran off to recover it for her. The rest of the group arrives on the scene, and later, the group returns to the Pokémon Center, where they are greeted by Nurse Joy and Charlie. Charlie announces to the group that he has made plans to visit the Kantonian Gym for tomorrow, and reveals that he is one of the Trainers there. Ash is immediately excited by the prospect, and he and his classmates unanimously approve the idea. Elsewhere, Team Rocket's kite is revealed to have gotten stuck in a tall tree, with Bewear having already run a great distance before noticing that she is only pulling along a string.