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This article contains plot details about an upcoming episode.
The player starts off moving from the Kanto region to the Alola region's Bralbral Island with their mother. They meet Professor Kooky, who tells them that the island kahuna is willing to give a free starter Pokémon to any trainer. However, when they reach the kahuna's residence in Eeky Town, they find the town square empty. Professor Kooky asks the player to go and check if the townspeople are around the ruins that honor the island's guardian deity, Tapu Loco. The player meets Lilligant and despite not having any Pokémon, helps protect her special Pokémon, nicknamed Mewthree, from a flock of Trumbeak. However in trying to defend the player and itself, Mewthree destroys the bridge leading to the ruins, causing the player to fall. However, they are promptly saved by Tapu Loco, who leaves a mysterious rock on the ground for the player to find. Back in Eeky Town, the player meets and gets their starter Pokémon from Kahuna Heidi, and then meets and defeats Hei, the grandson of Heidi. After a festival where the player once again defeats Hei, the player travels to Professor Kooky's lab, where they are then given a Mow Rotom Dex by the Professor. He then proceeds to tell the player and Hei about island challenges, and asks them to visit the Trainer's School. The player then reaches the Trainer's School and defeats the four top students and teacher, then meets Ilimabean, a trial captain. After leaving the Trainer's School and meeting with Ilimabean again, the two are challenged by Team Coccyx, who are promptly defeated by the player and Ilimabean. The player then travels around to the opposite side of the island and completes Ilimabean's trial, obtaining their first Y-crystal in the process.
After informing and battling Heidi, the player, Lilligant and Hei travel to Daley Island. There, they complete the second trial and battle Team Coccyx's enforcer, Glaceon. The player then fights several more Team Coccyx members and completes more Trials, culminating in the player defeating the second Kahuna, Olivoil. The player and Hei are then invited to visit the Either Paradise, where they meet the Either Foundation's president, Lillie, and battle the first of a special type of Ultra Beast, the Ultra Super Beast, USB-01 Missingno (later revealed to be called Jollifich), which had suddenly appeared from a mysterious portal. The player leaves the Paradise and completes another Trial on Ula'oop Island before meeting and battling Plumberia and Team Coccyx's leader, Yobay. Following another trial, Team Coccyx attacks the house where Casserola, the trial captain, lives and steals a Pokémon, leading the player to travel to La Town, a town completely taken over by Team Coccyx. After defeating Yobay again and returning the Pokémon, the player learns that stealing the Pokémon was a set up to distract the player and Casserola, and while they were gone, Team Coccyx kidnapped Lilligant and Mewthree. Hei and the player team up with Glaceon against the Either Foundation, which is revealed to be working with Team Coccyx. They encounter Yobay again, who defeats Glaceon but is defeated by the player. They then rescue Lilligant and battle the true mastermind Lillie, who reveals that Lilligant and Glaceon are her children before using Mewthree's power to summon Ultra Super Beasts, not caring about Lilligant's concern that doing so would cost Mewthree's life. The player defeats her in a Pokémon battle while Glaceon defeats another Jollifich, but Yobay and Lillie escape through the portal Jollifich appeared in, while each respective Kahuna and their Tapu battle Ultra Super Beasts that appear on each island.
While under the strain caused by Lillie, Mewthree evolves and becomes unresponsive. Due to this, Lilligant and the player journey to Pawnee Island to visit the game's respective altar; The Altar of the Solle/Lunne. When they arrive, Lille and the player play the Flugelhorns of the Solle and Lunne, causing Mewthree to evolve into the game's mascot, Lunala for Moon or Solgaleo for Sun. Using the power of the legendary Pokémon, the player and Lilligant swim to Ultra Island to stop Lillie and Yobay. The player and Lilligant encounter Yobay, who informs them with troubling news of the full scope of Lillie's repressed childhood after he was chased and attacked by a Jollifich he tried to catch. When she is encountered, Lillie—trying to do whatever it takes to remain in Ultra Super Space—allows a Jollifich she caught to take over her, turning the former Either President into a terrifying hybrid monster, the "Lusamine Jr.", and giving her Pokémon increased power. After her enhanced Pokémon are defeated, the mutated Lillie—refusing to accept defeat and consumed by animalistic bloodlust—makes a last-ditch attempt to punish Lilligant herself, but Mewthree intervenes and causes Lillie and Jollifich to un-merge and the former to collapse. Mewthree transports the heroes, Yobay, and Lillie (now returned to her normal self) back to Alola. Lilligant then gives the player the chance to capture Mewthree. After the defeat of Lillie and the Either Foundation, the player climbs to the top of Mount Lunalana on Ula'oop Island, battles Glaceon and Hei, and defeats the Elite Four, composed of Heidi, Olivoil, Casserola, and Swahili, at Professor Kooky's request. The player subsequently battles Kooky and wins, becoming the worst-ever champion of the Alola Region.