Pokémon Mystery Dungeon: Explorers (Nintendo Cinematic Universe)

Pokémon Mystery Dungeon: Explorers is a Japanese duology anime film.

Time and Darkness
Traversing time and darkness, a boy who has been turned into a Pokémon has to find a way to return back to normal.

Sky
During the events of Time and Darkness, the Wigglytuff Guild traverses the skies for more secrets behind the time disruption.

Time and Darkness

 * A Pokémon is washed ashore by a storm and is discovered by the partner, a timid Pokémon who dreams of forming an exploration team.
 * After teaming up to recover the partner's Relic Fragment from some bullies, the Pokémon, who has lost all memories except their name and the fact that they used to be human, agrees to form an exploration team to piece together their identity.
 * The two enlist at the Wigglytuff Guild and begin training as adventurers. During this time, the Pokémon discovers that they can have visions of the future or past.
 * Eventually, the authorities alert the guild that a criminal named Grovyle has been stealing artifacts called the Time Gears, which stabilize the flow of time in each region and cause time to stop when stolen. The Pokémon and partner attempt to intercept Grovyle, but are defeated.
 * Afterwards, the guild enlists the aid of a famous explorer named Dusknoir, who explains that the player's ability to see through time is called the Dimensional Scream. Dusknoir reveals that he and Grovyle are from the future and that if the Time Gears are stolen, the Pokémon world will become paralyzed and turn into a dark, dismal region filled with scared and corrupted Pokémon.
 * With assistance from the guardians of the Time Gears, Uxie, Mesprit and Azelf, Dusknoir successfully captures Grovyle and returns the Time Gears to their rightful places.
 * Back in town, Dusknoir opens a Dimensional Hole to take Grovyle back to the future to face justice and bids farewell to the villagers, but suddenly grabs the Pokémon and partner and drags them into the portal with him.
 * The Pokémon and partner awaken in a prison in the future. After escaping a near execution with Grovyle by Dusknoir, they discover the world is still paralyzed. They learn from Grovyle that the paralysis was caused because of the collapse of Temporal Tower, which also corrupted its head occupant, Dialga, into a tyrannical being known as Primal Dialga. Grovyle exposes Dusknoir as a villainous agent sent to the present to capture him and reveals that he and a human companion traveled back in time to take the Time Gears to Temporal Tower in order to save the world; this human is actually the Pokémon.
 * With the help of Celebi, a friend of Grovyle, the group manages to escape Dusknoir's group and return to the present.
 * Grovyle reveals that, while it is true that time stops when a Time Gear is taken (not "stolen"), this effect is only temporary and that once the Time Gears are returned to Temporal Tower, time is permanently restored in all locations.
 * Arriving back to the present, the group enlists the help of the guild to take the Time Gears to Temporal Tower to restore time. While Grovyle gathers the Time Gears, the guild investigates Temporal Tower and discovers a way to reach the Hidden Land where it lies, using the partner's Relic Fragment.
 * The Pokémon, the partner, and Grovyle travel to the Hidden Land, and are accosted by Dusknoir. He reveals to the Pokémon that if they succeed in changing the future, they and Grovyle will be erased from existence.
 * Grovyle sacrifices himself to drag Dusknoir back to the future, and the Pokémon presses onward. He and the partner make their way to the top of Temporal Tower, defeat Primal Dialga and restore it to sanity, and replace the Time Gears and stop the planet's paralysis.
 * On the way back, the Pokémon says a final goodbye to the partner before vanishing.
 * Dialga is deeply moved by the partner's grief over the Pokémon's death, and restores the Pokémon to the timeline as thanks for bringing time back under control. The Pokémon reappears at the beach and reunites with the overjoyed partner.
 * Sometime later, the player and partner graduate from Wigglytuff Guild and move their base of operations to Sharpedo Bluff, the partner's old home. In Luminous Spring, they learn that neither the partner nor the Pokémon can evolve due to a distortion in space. After many missions and explorations, it is revealed that Darkrai was responsible for the events of time and darkness.
 * The team, with the help of Palkia and Cresselia, defeats Darkrai, fixing the distortion and finally allowing the Pokémon and partner to evolve.

Sky

 * Long ago, Igglypuff, later known as the head of the guild Wigglytuff, became an explorer by meeting Armaldo, and began his journey as one. From that moment, he showed his prodigious talent for exploration and succeeded in one difficult expedition after another. However, Armaldo was arrested for being a criminal himself, resulting in affecting Igglypuff for years to come.
 * Igglypuff, now evolved as Wigglytuff, meets the Team Charm in one of his explorations.
 * The treasure hunter Team Charm, formed by Lopunny, Gardevoir, and Medicham, have previously heard of a treasure in the south of the continent. After confronting numerous foes, they went on finding the rumored treasure, only to be a dud made by Ditto. The real treasure was none other than a Time Gear.
 * Long after these events, Bidoof, one of the members of the Wigglytuff Guild, originally wanted to become a first-class explorer. As such, he left his hometown and started training at the guild, with mild results and seen as the idiot of the group. It is in an exploration of a rumored treasure that he meets Jirachi, with both of them being the reason behind Pokémon and their partner joining the Guild soon after.
 * During the chase against Grovyle, Sunflora, a senior member of the guild, got a request on arresting a group of Haunters.
 * As Grovyle sacrifices himself to drag Dusknoir back to the future, it was originally thought that Grovyle, the Pokémon from the future, will disappear as a result of Pokémon's success in changing the future. However, the both of them, along with Celebi, were also involved in the change.
 * Primal Dialga had finally made its own move to prevent the future from being changed.
 * Grovyle is determined to stop Primal Dialga from keeping the dark future intact, while Dusknoir is determined to find out the truth from Primal Dialga's betrayal.
 * After the team graduated from the Wigglytuff Guild, they were made aware that a village was discovered at the east of the continent. By getting there, they find a village filled with Shaymins, numerous explorers including teams, and a mountain in front. Atop of the mountain was once a field to see across the continent turned into a poisonous area.
 * Pokémon eventually fixes this problem by reaching the peak, reverting back to its original intent.

Time and Darkness

 * Based on Pokémon Mystery Dungeon: Explorers of Time and Explorers of Darkness.

Sky

 * Based on Pokémon Mystery Dungeon: Explorers of Sky.