Following the adventures of the first Chocobo Dungeon game, Chocobo and Mog continue to search for treasure. One day, Mog discovers a new Mysterious Dungeon and takes the treasure from inside. This releases a seal which causes the Bahamut to appear just as the dungeon plunges into the ocean. Chocobo is rescued by a young white mage, Shiroma, who is the only human living in the monster village. Chocobo must help Mog, find Bahamut and fix whatever has been unsealed from the Mysterious Dungeon.