The game begins on Million Island, where Chocobo arrives by boat. Named for its worth of one million gil, Chocobo soon finds out that the island has its own set of problems. The owner, Cid, is well-known for his picture books, but has suddenly fallen ill in the process of writing his latest story. Meanwhile, a mysterious girl washes up on Million Island, and a witch simultaneously appears to destroy the happy endings in Cid's picture books. It falls upon Chocobo to uncover the mystery behind these strange happenings and combat the evil which befalls the island. With the girl as a guide, he travels through the worlds of Cid's picture books to restore peace within them, working with the heroes he meets along the way to defeat the witch and uncover the truth behind Million Island.

Much like its predecessor, the gameplay of Majo to Shōjo to Gonin no Yūsha revolves heavily around mini-games and the occasional battle. Completing the basic objective in each mini-game will move the story forward, though completing the two more challenging objectives may earn you more cards for battle. Battles are done in the style of a card duel, where Chocobo must build up a deck that may summon powerful monsters to defeat the various bosses that stand in his way.
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