"Pokémon Mystery Dungeon: Toki to Yami o Meguru Saigo no Bōken" is a special anime episode based on the "Pokémon Mystery Dungeon" spin-off game series. The story centers on a human who is transformed into a Pokémon, specifically a Squirtle, and their partner, a Charmander. Together, they form a rescue team dedicated to helping other Pokémon in need. The narrative begins with the duo receiving a mission to investigate a mysterious time gear, an artifact that maintains the flow of time in the world.

As the story progresses, the rescue team discovers that the time gears are being stolen, causing time to stop in certain areas. This disruption threatens the balance of the entire world. The team learns that the thefts are orchestrated by Grovyle, a rogue Pokémon working alongside Dusknoir, a shadowy figure from the future. Grovyle’s actions are initially perceived as malicious, but it is later revealed that he is attempting to prevent a catastrophic event known as the planet’s paralysis, which would freeze time permanently.

The protagonist and their partner eventually ally with Grovyle to confront the true antagonist, Dialga, the legendary Pokémon of time. Dialga, corrupted by the disruption of the time gears, has become a destructive force. The rescue team, alongside Grovyle, must journey to the heart of Temporal Tower to restore the time gears and confront Dialga. The climax involves a battle against Dialga, during which Grovyle sacrifices himself to ensure the protagonist can complete the mission.

The story concludes with the restoration of time and the protagonist returning to their original human form, leaving behind their Pokémon partner and the world they had come to cherish. The narrative explores themes of friendship, sacrifice, and the consequences of tampering with natural order, all set within the unique framework of the Pokémon Mystery Dungeon universe. The main characters—Squirtle, Charmander, Grovyle, and Dusknoir—are central to the emotional and action-driven plot, each contributing to the resolution of the overarching conflict.