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.

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.