In a world where Pokémon coexist and communicate freely, ancient artifacts called Time Gears maintain the flow of time in each region. Removing one halts time in that area, so even the most wicked Pokémon avoid stealing them. Lately, odd disruptions in the timeline have caused Mystery Dungeons to appear and increased hostility among Pokémon. Teams form to explore these dungeons, subdue the aggressive creatures, and restore peace.
The current time disturbances are not from recent thefts of the Time Gears, but from the slow collapse of the Temporal Tower and Dialga turning into Dark Dialga. Juptile, the notorious thief, has stolen the Time Gears intending to bring them to the Temporal Tower to prevent its ruin. Team Pokédans, made up of Hikozaru and the former human Pochama, must join forces with Juptile to travel to the Phantom Land where the Temporal Tower stands. If they fail, the tower will fully decay, freezing the entire world in time forever.