This entry in the Pokémon Mystery Dungeon series once again puts the player in the role of a human who has turned into a Pokémon and lost their memory. This time, the player character ends up in Serene Village, where they are enrolled in the local school and meet a troublemaking classmate who becomes their close friend. The two eventually leave home to join the Expedition Society in Lively Town, where they begin to hear rumors of a malevolent force turning Pokémon to stone. From there, the children begin an adventure that will not only decide the fate of the world, but reveal the truth of their mysterious pasts.
New features in this game include stones called emeras, which can be placed into a held looplet to provide beneficial effects such as buffs and Mega Evolution. The series' bulletin board system for taking missions is replaced by the Connection Orb, which continually opens up new jobs as more Pokémon are befriended. This also serves as the recruitment mechanic for the game, and allows the player to add main characters from past Pokémon Mystery Dungeon games to their team. Certain locations from previous games may be visited as well.