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There are five Special Episodes in Pokémon Mystery Dungeon: Explorers of Sky where the player can branch off from the main storyline and explore other aspects of the Mystery Dungeon world, like other characters and new locations.
Special episodes are unlocked after completing certain parts in the main storyline. Special episodes can be started by going to the top menu and selecting "Episodes List". The player can continue a special episode by selecting "Continue" and then "Special Episode". All of the items stored in the Kangaskhan Storage and all Poke from the Duskull Bank can be jointly accessed through the main story and the special episode. After the player completes the episode, all items obtained throughout the episode will be stored in the Kangaskhan Storage and all Poke will be stored into the Duskull Bank.
- Set In: Past
- Main Character: Igglybuff
- Parteners: Banette, Skorupi, and Armaldo
- Dungeon: Murky Forest, Eastern Cave, Fortune Ravine
- Set In: Past
- Main Character: Lopunny
- Partners: Gardevoir and Medicham
- Dungeons: Southern Jungle, Boulder Quarry, Right Cave Path, Left Cave Path, Limestone Cavern