There are fabled gems known as the Time Gears that manage the passage of time in their respective places in a world where Pokémon dwell and converse with one another. If one is stolen from its resting place, time stops in that region, making even bad Pokémon afraid to steal them. However, time anomalies have suddenly appeared throughout the area, resulting in the development of Mystery Dungeons and deadly Pokémon. Pokémon exploration teams have been organized to investigate these Mystery Dungeons, apprehend dangerous Pokémon, and keep the peace. It turns out that the temporal anomalies were created not by the recent departure of the Time Gears, but by the Temporal Tower steadily crumbling and Dialga corrupting.