At Professor Kukui's house, Kukui realizes Professor Burnet and Munchlax left their lunches behind. With Kukui needing to attend the Pokémon Battle Study Conference, Ash offers to deliver the lunches to Aether Paradise for him. When Kukui leaves, Lillie and Hobbes arrive aboard a jet. Hobbes explains that Lusamine has been busy since the end of the Manalo Festival, and asks Ash if he could visit her to report his side of the story, which he agrees to do.
Ash, Lillie, and Hobbes arrive at Aether Paradise. Team Rocket is also there, disguised as Aether Foundation Employees with the intention of capturing the facility's Pokémon. When Faba notices Team Rocket and interrogates them, Wicke arrives and explains that she recently hired them as Conservation Area employees. As Faba walks off, Wicke hands Jessie a clipboard to begin counting the Pokémon. Meanwhile, James is assigned cleaning duty, but soon becomes exhausted. He calls on Mareanie's assistance, and after poisoning James, she mops the floors with her tentacles. Meanwhile, Meowth is taking a break and listening to several Whimsicott explain the relaxing life they enjoy at Aether Paradise. Meowth has a fantasy of Giovanni surrounded by the Aether Paradise Pokémon, and tells the Whimsicott that they will enjoy living with the Boss.
Elsewhere, Burnet and Munchlax are ecstatic to have their lunches now with them. Then Rotom uploads its Manalo Festival data onto the Aether Foundation's system. Wicke offers Ash a tour of Aether Paradise, and the young Trainer happily obliges. Elsewhere, with the Pokémon all accounted for, Team Rocket agree to start their large scale plan but are interrupted when Ash arrives on the scene. Pikachu looks up at Team Rocket, and the trio quickly flees to avoid being detected. However in their escape, the list of Pokemon flies out of Jessie's back pocket and lands at Faba's feet. Ash and Lillie enter the Ditto play space, and one of the Ditto approaches Pikachu and soon transforms into him, only it still maintains its facial expression. Wicke adds that the Ditto is almost ready to graduate. The term "graduate" perplexes Rotom and Ash. Burnet explains that they care for the Pokémon at Aether Paradise before returning them to the wild. As Team Rocket walk down a corridor a Stufful starts following the group. Meanwhile, Faba runs over to Lusamine with the count list in hand, and he exclaims that Stufful is unaccounted for. Then Lusamine, Wicke, Brunet, Ash and Lillie agree to split up and search for Stufful. Rotom's Pokédex on Stufful entry alarms Ash, but Wicke and Burnet assure him that Stufful is harmless. In a flashback, Wicke explains that she first met Stufful during one of her solo patrols. She heard its cries and soon found Stufful was trapped under a fallen tree. In an act of desperation, Wicke dug through the dirt to make a gap big enough to rescue Stufful. Wicke tears at the thought of Stufful going missing, so the search party begins.
Team Rocket continues to walk away from Stufful and eventually stop. Jessie questions why it's following them, but James then suggests that Jessie should catch Stufful. Jessie throws her Poké Ball, but Stufful sidesteps it. She tries a second Poké Ball, but Stufful ducks this time. Jessie attempts to capture Stufful for a third time, but the Pokemon headbutts the Poké Ball into Jessie's face. Jessie scolds Stufful, but the Pokémon instead jumps onto Jessie's face and begins smothering her. Wicke, in a frantic voice, makes an announcement over the loudspeakers to alert everyone that Stufful is missing from the Conservation Area. Meowth and James overhear the announcement and fear that they will be caught red-handed attempting to steal Stufful and lose their chance to catch all the other Pokémon. Meanwhile, Jessie struggles to free herself of Stufful, and the Flailing Pokémon manages to latch itself onto Jessie's hair. As Ash and Lillie appear behind them, Team Rocket are run away to maintain their covert operation. The group rush passed Faba, who quickly notices Stufful attached to Jessie's hair. Team Rocket are eventually stopped on a walk bridge and surrounded by Lusamine, Wicke, Burnet, Faba, Lillie and Ash. Faba demands to know why the thieves ran, with the accusation shocking Team Rocket. The quartet contemplates their actions and they decide to launch into their motto.
With their true identities now exposed, Rotom demands that Stufful be returned. Jessie yells out that she would return Stufful, but it is attached to her. The answer only infuriates Ash, and he has Pikachu launch a Thunderbolt attack. As the electricity begins to reach into the air, Bewear crashes through the glass ceiling to rescue Team Rocket. As it is about to scoop up the group, Stufful captivates Bewear's attention. Suddenly Bewear lets out a shrill of joy, and Stufful jumps into its arms. The scene shocks everyone, and Meowth reveals that Bewear is Stufful's mother. Everyone is overjoyed for the pair, and Stufful waves to Wicke and the others. Bewear does the same before bundling Team Rocket in her arms and jumping onto an Aether Foundation helicopter. Bewear breaks off the helicopter's rotor blades and hands it over to Stufful. Stufful promptly begins twirling the blades in its hands, and this allows Bewear to return to her Melemele Island den. Wicke, in particular, is relieved to see Stufful returned to its mother's arms and takes a moment to reflect.
Sometime later, there is another hole in the Conservation Area's roof, and helicopter blades sit atop a tree canopy. Wicke walks through the Conservation Area and stops after spotting a leaf full of honey lying on the ground. The mysterious gesture startles her, but the culprit is not revealed.