At the Pokémon School, Ash and his classmates are greeted by Faba, much to their confusion. He explains that Lusamine had asked him to come to teach them about science. Ash is intrigued, and Faba begins his lesson by bringing in a strange machine of his own design, dubbed the "Super Duty Tidy-Up Faba Deluxe". He then shows the class an everyday Poké Ball, and lectures about its unique ability to compress even the largest and heaviest of Pokémon, like an Alolan Exeggutor or a Snorlax, into an easily portable size. As everyone realizes that he has a point, Faba brings their attention back to his invention, which uses the same principle as a Poké Ball to shrink down an object of any size and store it into a small, Poké Ball-like capsule. This allows the object to be transported anywhere the user wishes, and then be returned to its normal size by simply opening the capsule, making moving things a breeze.
The class is amazed and Ash asks Faba for a demonstration. Gladly agreeing to this, Faba turns his machine towards the class blackboard and fires, but nothing happens. He fires the machine a couple more times, with disappointingly lackluster results. Faba is baffled as the machine worked perfectly during his lab tests. Following Professor Kukui's suggestion, Faba reboots the machine and attempts to fire it again. However, the machine suddenly goes haywire, and ends up shooting its beam towards the ceiling, from which it starts bouncing all around the classroom. Everybody seeks shelter as the beam continues to bounce back and forth, until it finally hits Ash, Lillie, and Sophocles, who had all hidden under the same desk, causing them to seemingly disappear. Kukui asks if they wound up in a capsule, but Faba responds that the machine shut down. All of a sudden, Ash, Lillie, and Sophocles's voices start calling out to everyone. Pikachu looks underneath the desk and he finds the trio have shrunken down into inch-high miniature versions of themselves. Faba assures everyone that everything is under control, saying that this can be solved with the machine's capsules. One by one, he places each of the shrunken children into a transparent capsule and says that they'll return to normal once he lets them out. He opens the capsules, but in a few seconds, it becomes evident that this method isn't working. Faba starts panicking when he thinks about how angry Lusamine will get over this and asks for Rotom's help in checking the machine.
Ash and Lillie use the opportunity to enjoy a joyride on Pikachu's back around the classroom. Seeing this, Togedemaru starts rolling around the desk with Sophocles balanced on her rolling body. As Faba and Rotom continue checking the shrinking machine, Togedemaru falls off the desk and begins to bounce around, accidentally hitting the shrink ray and breaking it. She then collides into Pikachu, causing her, Ash, Lillie, and Sophocles to be sent flying out of the classroom and into the pond outside the school. They are soon sucked into a vortex, which leads to the roadside drainage and washes them away. Kiawe tries to get the sleeping Rowlet to wake up and help them, but even when thrown outside, it stubbornly remains asleep, flying upside down in the air. With Professor Kukui's permission, Kiawe, Mallow, and Lana enter the Ultra Guardians base and take to the skies on board their Ride Pokémon to search for their friends. Rotom attempts to join in, but Faba reminds it that it has to stay at the school to help repair the machine.
Meanwhile, Ash, Lillie, and Sophocles are still floating down the river on top of Togedemaru. While Lillie is worried about them getting further away from the school, Ash is enjoying the experience. Suddenly, the ground starts shaking, which alerts the group to a Mudsdale wading through the river. The massive Pokémon causes a tidal surge that washes the shrunken students ashore. Lillie notes that at this size, even the smallest of things can turn into an adventure. Suddenly, an Alolan Rattata appears and inspects them, but Togedemaru uses her spikes to send it scurrying off. While Ash and Sophocles thank Togedemaru, Lillie ties up her hair as a sign of determination, declaring that she's prepared to live at this size. Sophocles is freaked out by the idea, but Ash agrees with Lillie, saying that it could actually be fun. They are then approached by a small group of Dedenne, which start communicating with each other through their whiskers. Togedemaru starts producing sparks from her own checks, and the Dedenne quickly gather around her, all of them now communicating together. These same signals reach Pikachu and Snowy, who are in the midst of a search, and the two Pokémon start heading towards the source of the signals.
Sophocles is feeling increasingly uncomfortable and pleads for them to return to the Pokémon School. Lillie, on the other hand, is imagining what their tumultuous life as shrunken-down school students would be like; from how hard writing with regular-sized pencils will be, to how impossible the once-simple task of jumping a rope would become. Now outright panicking at the thought of having to stay small forever, Sophocles again pleads for them to return to the school. Ash and Lillie, meanwhile, have decided to have a bit more adventuring before that, and are now hanging onto a floating Comfey, urging Sophocles to come along. Not wanting to be left alone, Sophocles pursues the pair while on Togedemaru's back. Soon, Ash and Lillie are floating over the streets of Hau'oli City, thoroughly enjoying the experience. Unbeknownst to them, they are noticed by a certain Alolan Persian, who seems to recognize Ash, licking its lips. Elsewhere, Kiawe, Mallow, and Lana are having trouble in locating their minuscule friends, but they soon spot Pikachu and Snowy communicating with the group of Dedenne from before and decide to follow their lead.
As the sun starts to set, Ash and Lillie realize that they can't see Sophocles following them anymore. Their concerns are quickly subsided by more pressing matters, as a Murkrow swoops them several times, causing the pair to lose their grips on the Comfey and fall. They bounce off the canvas rooves on the market stalls, until they hit a palm tree frond, which sends them straight into a fruit stall. They quickly find out that the stall in question belongs to Anela, who doesn't seem to be too surprised to see them in their shrunken state. The reason for this is quickly revealed as Ash and Lillie spot Sophocles sitting on a weighing scale below them and eating an apple. Anela offers them an orange, but Lillie points out that they're too small to even peel off the fruit's skin. Suddenly, under Ash's weight, the oranges start falling into the street. The scale that Sophocles was sitting on is knocked down by the avalanche of fruits and hits Togedemaru, knocking her out as she also rolls into the street.
While Anela asks people around the street to help her pick up the oranges, Ash, Lillie, and Sophocles have managed to avoid being hit by the falling fruits. The Alolan Persian from before then appears, stopping the unconscious Togedemaru's rolling. Ash immediately recognizes this Persian as the same one who once bullied Litten. Persian knocks Togedemaru towards the three children, who start running for their lives. Although the three manage to avoid being squashed by climbing onto the sidewalk, Persian is still after them. Meanwhile, Mallow finds Togedemaru, and then informs Kiawe and Lana who are out searching in elsewhere in the city.
Ash, Lillie, and Sophocles run away from the persistent Persian through alleyways, but soon find themselves facing a dead end. Ash picks up a stick in a desperate attempt to fight back, but before Persian can even attack them, it is struck from behind by a Magical Leaf from Mallow's Tsareena, much to the cornered kids' delight. As the three retreat to a safer distance, Tsareena and Persian start clashing, with Tsareena easily gaining the upper hand with her powerful kicks, impressing everyone. As Persian attacks again, Mallow orders Tsareena to use Trop Kick, which sends Persian straight into a wall. When Persian tries to get up, Tsareena stomps on its face to show off her dominance. Despite all this, Persian remains defiant, so Tsareena, clearly annoyed by this, uses Magical Leaf to shave off some of the furs on its back, causing Persian to finally lose its will to fight and scurry off in tears. Mallow compliments Tsareena, saying how she's starting to act more like an adult.
Just then, Togedemaru rushes in, and Sophocles runs towards her to greet her, only to almost be crushed under her weight. Pikachu, Snowy, Kiawe, and Lana also arrive, happy to see each other again. Kiawe explains how they used Pikachu and Snowy to find them, and Ash and Lillie thank their respective Pokémon. However, Ash petting Pikachu on his nose causes the Mouse Pokémon to sneeze at the three, sending them flying. Then, unexpectedly, the three start to glow and grow, and before anyone knows it, they're back to their normal size. They happily hug their respective partner Pokémon, and Lana laments that all's well that ends well, but Mallow and Kiawe are confused about how Pikachu's sneeze could've restored them. Elsewhere, Persian's owner is horrified to see the bruised and shaven state her pet is in.
Back at the Pokémon School, Ash, Lillie, and Sophocles are going over their experience, with Sophocles being the only one of the three to not have found the experience pleasant. And while everybody was away, Faba and Rotom have completed the repairs on the shrink ray. Faba apologizes for the incident before resuming his demonstration on a chair. However, as he attempts to fire the machine, it once again goes awry and ends up firing its beam at Togedemaru. For a moment, nothing happens, but then, instead of shrinking, Togedemaru starts to grow, causing everyone to panic. Faba is unable to do anything to stop it, and only seconds later, Togedemaru's giant body bursts out of the side of the school building, just as her growth comes to a stop.