At the Pokémon School, Ash and his classmates are greeted by an unexpected visiting teacher: Faba. Lillie asks why he is here, and Faba tells that Lusamine asked him to come teach them about science. Ash asks what kind of science he's planning to teach them, and Faba responds by bringing in a strange machine of his own design. He then brings out an everyday Poké Ball, and asks the class if they've ever thought of how much of a great work of science they actually are, being able to take Pokémon as big as an Alolan Exeggutor or as heavy as a Snorlax and compress them into an easily portable size. The class understands that he has a point, which brings Faba back to his invention: using the same principle which a Poké Ball uses to shrink a Pokémon, he has developed this device, dubbed the "Super Compressor Faba DX", which can take an object of any size, like a house, shrink it down, 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 legitimately excited, and Ash asks Faba to show them how the machine works in practice. Gladly agreeing to this, Faba turns the machine towards the class blackboard and fires, but the beam fired by the machine has no effect on it whatsoever. He fires the machine a couple more times, with equally lackluster results, much to his audience's disappointed and his own bafflement, since the machine worked perfectly during his tests. Professor Kukui suggests rebooting the machine, which Faba proceeds to do, after which he tries firing it again. However, the machine suddenly starts going awry, and its beam ends up getting fired towards the ceiling, from which it starts bouncing all around the classroom. Everybody seeks for shelter as the beam continues to bounce back and forth, until it finally hits Ash, Lillie, Sophocles, who had 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, Sophocles's voices start calling out for everyone, and Pikachu looks underneath the desk, finding the three, having shrunken down into inch-high miniature versions of themselves.
Soon, the three shrunken children are standing on the desk, still trying to process fact how small they've become. Kukui compares this to the Pokémon move Minimize, and Kiawe urges Faba to do something about the situation. Faba assures 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 the transparent capsules, 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 Rotom's help in checking the machine. Togedemaru approaches Sophocles to comfort him, while Ash and Lillie are riding on Pikachu, who starts running around the classroom with them on his back. Seeing this, Togedemaru places Sophocles onto herself and starts rolling around the desk with him balancing on her rolling body. As Faba and Rotom continue checking the shrinking machine, Togedemaru falls of the desk and begins to bounce around, accidentally hitting the shrink ray and breaking it. She then falls straight into Pikachu, causing her, Ash, Lillie, and Sophocles to be sent flying out of the classroom and into the pond outside the school. For a moment, it looks like they're safe, but they soon get sucked into a vortex, which leads them to the stream running down the road, which washes them away. Kiawe tries to ask help from the sleeping Rowlet, even throwing it outside, only for Rowlet to continue sleeping while flying upside down in the air. Kiawe asks Professor Kukui's permission to use the Ultra Guardians to help, and Kukui agrees. Rotom attempts to join in, but Faba reminds it that it has to remain to help him with the machine. And so, like several times already, Kiawe, Mallow, and Lana enter the Ultra Guardians base and board their Ride Pokémon, quickly taking it to the skies to start searching for their friends.
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 actually starting to enjoy the experience. Suddenly, the ground starts shaking, its cause being a Mudsdale wading through the river. The massive Pokémon causes a wave to wash over the three shrunken group, and are washed ashore by it. Lillie muses how at this size, even the smallest things can turn into an adventure. An Alolan Rattata appears, inspecting them, but Togedemaru uses her spikes to attack it, sending 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 freaks out at this idea, but Ash agrees with Lillie, saying that it could actually be fun. They are then approached by a small group of Dedenne, who start communicating with each other through their whiskers. Togedemaru starts producing sparks from her own checks, and the Dedenne quickly gather around her, communicating amongst themselves and her. The electric signals produced by them are picked up by Pikachu, who is searching for the group along with Snowy, and they start heading towards the location where the signals are coming from.
Sophocles is feeling more uncomfortable by the second 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 would have become, to how impossible the once-simple task of jumping a rope would be. Sophocles, now outright panicking at the thought of having to live the rest of his days at this size, pleads to return to the school and never returned to normal. Ash and Lillie, meanwhile, have decided to have a bit more adventuring before that, and are now hanging on to a floating Comfey, urging Sophocles to come along. Not wanting to be left alone, Sophocles starts riding Togedemaru and following them. 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 miniscule friends, but they soon spot Pikachu and Snowy communicating with the group of Dedenne from before, and then following their lead. Figuring that the two Pokémon must have a lead, the flying trio decides to follow them.
As the sun is starting to set and the evening comes, Ash and Lillie realize that they can't see Sophocles following them anymore. However, their attention is then caught by a Murkrow, which repeatedly attacks them, causing them to lose their grips on the Comfey and fall. They bounce off the canvases on the markbe rok stalls, until they hit a palm tree, which sends them straight into a fruit stall. They quickly find out that said stall belongs to Moani, who doesn't seem to be too surprised to see them in their shrunken state. The reason for this turns out to be Sophocles, who's eating an apple while sitting on a scKe below them. Moani tells them to have an orange, but Lillie points out that they're too small to even peel off the skin of the fruit. Unexpectedly, the oranges start falling down under Ash's weight and rolling all over the street. The scale that Sophocles was sitting on is knocked down by the falling fruits and hits Togedemaru below, knocking her out and sending her rolling into the street too.
While Moani asks people around the street to help her pick up the fallen fruits, Ash, Lillie, and Sophocles have managed to avoid being hit the orange slide. The Alolan Persian from before then shows up, 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 they manage to escape from being squished by climbing up to the sidewalk, Persian is still after them. Meanwhile, Mallow finds Togedemaru, and contacts Kiawe and Lana on other locations around the city, informing them of her find and saying that Ash and the others must be nearby as well.
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 more safer distance, Tsareena and Persian start clashing, with Tsareena easily gaining the upper hand with its 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 over it. However, despite all this, Persian is still willing to keep going on, so Tsareena, clearly annoyed by this, uses Magical Leaf to shave off some of the fur 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 at her to greet her, only to almost be crushed by 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 of how Pikachu's sneeze could've restored them. Elsewhere, Persian's owner is horrified to see the look 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 said experience pleasant. And while everybody was away, Faba and Rotom have completed the repairs on the shrink ray, and Faba, after apologizing for the trouble he had inadvertently caused, declares that he will now properly demonstrate his device on a chair. However, as he attempts to fire the machine, it once again goes awry, and ends up pointing at Togedemaru, who is hit by the beam fired from it. For a moment, nothing happens, but then, instead of shrinking, Togedemaru starts to grow instead, causing everyone to panic. Faba is unable to do anything to stop it, and only seconds later, Togedemaru bursts through of the school wall, just as her growth comes to a stop, with her giant body now sticking out of the side of the school building.
