Pokémon Super Mystery Dungeon (Nintendo Cinematic Universe)

Pokémon Super Mystery Dungeon is a Japanese anime film.

Summary
A boy trapped in the body of a Pokémon joins the Expedition Society to save the world one last time.

Plot Elements

 * A boy wakes up transformed into a Pokémon and only remembering that they used to be a human. When he are suddenly attacked by a group of Beheeyem, a friendly Nuzleaf helps them escape, gives them shelter in Serene Village, and enrolls them in a school for young Pokémon. There, he meet their partner, who dreams of joining the Expedition Society but has become the town pariah due to his overeager nature.
 * Taking advantage of the Pokémon not knowing the area, school bullies Pancham and Shelmet trick Pokémon (and the partner, to their chagrin) to enter a mine owned by a Gabite, but the local Drilbur defuse the situation before it gets out of control.
 * Several days later, the other kids ask Pokémon where they're from, having ascertained that they can't feasibly be Nuzleaf's kid. Not wanting to hide the truth, Pokémon reveals what they remember, but Pancham gets everyone (except the partner and the school principal) to think they're a pathological liar looking for attention.
 * The next day, Nuzleaf's neighbor, Roselia, arrives at the school looking for her daughter Budew, who's disappeared without any real explanation.
 * Recalling a conversation they had with the partner's father about a special honey that Budew overheard, Pokémon and partner rush to a nearby meadow and save her, winning the respect of their classmates and the town. That night, the partner sympathizes with Pokémon's outsider status and gives them one of the Harmony Scarves he has as a sign of friendship.
 * They eventually meet Ampharos, a member of the Expedition Society who gives them a Connection Orb and names them junior Expedition Society members. After saving Pancham and Shelmet from a group of Litwick who came to town to feed on their fears, Nuzleaf informs the pair that he wants them to join him to explore Revelation Mountain, a local mountain range the town has guarded for years with no reason why. However, the Beheeyem are spotted outside the village, forcing Pokémon and partner to flee to Lively Town, the site of the Expedition Society headquarters.
 * Upon arriving, Ampharos inducts them into the Expedition Society and introduces them to the other members: explorers Archen, Bunnelby, and Buizel; archaeologist Mawile; astronomer Jirachi; communications officer Dedenne; and cook Swirlix. After a few days of work, Archen invites them to a trip to the Air Continent, where they discover that a malicious entity has been turning Pokémon to stone.
 * The Society initially assumes Entei is involved after Latios and Latias are found turned to stone, but when Pokémon and partner inexplicably evolve to their final forms and defeat him, they realize he was only investigating the current events.
 * A few days later, the entity confronts Entei.
 * Although the Society is unable to prevent Entei from being turned to stone, they find evidence that implies that Krookodile, a local thug, is the culprit. When it is found that a dungeon called the Prehistoric Ruins may help them find more answers, the Society initially intends to go, but Pokémon and partner hear that Krookodile is headed towards Serene Village and leave with Archen to intercept him. Nuzleaf meets up with them and informs them that Krookodile was heading up Revelation Mountain and joins the chase.
 * At the top, the group discovers a sealed spring that can return petrified Pokémon to normal. They confront Krookodile, but Krookodile reveals that Nuzleaf paid him to go to Revelation Mountain.
 * Nuzleaf reveals himself to be the culprit behind the Pokémon turning to stone and, along with the legendary Pokémon Yveltal, petrifies Pokémon, partner, Archen, Suicune and Raikou; dries out the spring water; and begin attacking Pokémon around the world.
 * Ampharos, Jirachi, and Espurr manage to survive while everyone else in Serene Village and Lively Town are turned to stone.
 * During this time, Pokémon wakes up in a world called the Voidlands and is reunited with most of the Society. As they try to find a way back to their world, they discover that the planet's life source, the Tree of Life, was once pulled toward the sun by the entity, now known as Dark Matter, but was stopped by 'the alignment of the stars'. However, they are attacked by manifestations of the Voidlands' darkness.
 * Raikou, Entei, and Suicune save Pokémon, partner, and Mawile, but the others are incapacitated. They make their way up Reverse Mountain, the only way out of the Voidlands, but the battle at the top is so fierce that Pokémon and partner's allies have to sacrifice themselves to let them escape.
 * Pokémon and partner return to the Society headquarters where they reunite with Espurr, but are confronted by an escaped Beheeyem, who informs them that Dark Matter feeds on the negativity of others and can possess Pokémon. He also mentions that he believes the Tree of Life to be in the deepest part of the Prehistoric Ruins. He leads Pokémon and partner to the ruins, but when they reach the depths, they realize that Nuzleaf, anticipating Beheeyem's betrayal, lied about the Tree's true location.
 * Nuzleaf reveals that Beheeyem was responsible for Pokémon's memory loss, and Espurr is revealed to be a double agent for Nuzleaf.
 * Nuzleaf then tries using the room's energy to attempt to send Pokémon to the deepest part of the Voidlands. Ampharos, Jirachi, and Celebi intervene and transport Pokémon, partner and Espurr, who was actually a double agent for Ampharos, to the Tree of Life.
 * Celebi explains that Pokémon might have been summoned once before by Mew and the Harmony Scarves protect its wearers from turning to stone when near the Tree of Life. Upon reaching the end of the forest, they find the Tree of Life near dead. They are confronted by Yveltal, Nuzleaf, and the remaining Beheeyem, whom Dark Matter has corrupted. They turn the escaped Beheeyem to stone and try to turn the group to stone as well, but the group are protected thanks to the harmony scarves.
 * The group manage to defeat them and free them from their brainwashed state, but the battle allowed Dark Matter, who was inside the Tree of Life, to get the energy needed to pull the Tree out of the ground and send the planet toward the sun.
 * However, various flying Pokémon stall the ascent long enough for Arceus to send the player and partner into the Tree of Life. With help from Yveltal and the others, the two battle and destroy Dark Matter.
 * The Society and Xerneas, the physical form of the Tree of Life, congratulate them, but Pokémon soon becomes worried that they might be forced to leave the Pokémon world. When expressing their concerns to the partner, the partner informs them that, upon talking with Xerneas, they are the reincarnation of Mew and have to leave the world instead. The partner tells Pokémon to not be upset before departing in a ball of light.
 * Post-Credits Scene: Pokémon wakes up, now a human again, and recalls this to be the fifth Pokémon dream he's had, implying that was the same main character from the other Mystery Dungeon films.