Mirai Asahina, a 13-year-old girl who's going into her second year of middle school, witnesses a mysterious object fall in to the park. Excitedly, she brings her stuffed bear Mofurun with her to see what it was. When she gets there she sees a girl named Riko flying on a broom. Mirai has a lot of questions, and Riko explains that she's searching for something. The two of them are wearing similar pendants. Then Batti, an ally of the dark magic user Dokurokushi, appears before them and demands the "Link Stone Emerald." Batti creates a monster called a "Yokobaru" and drives them into a corner. Mirai, Riko, and Mofurun join hands and speak the magic words "Cure-Up Rapapa," their pendants glow, and they become the legendary Precure.

During her second year of middle school, Mirai Asahina, a girl excited by various things, goes with her stuffed doll Mofurun to investigate a mysterious object that fell from the sky. There, she meets a young magician named Riko, who wears a pendant similar to the one Mirai has and is searching for something known as the Linkle Stone Emerald. When dark servants of the evil witch Dokuroxy come seeking the Linkle Stone Emerald, Mirai and Riko join hands with Mofurun and transform into the Legendary Magicians, the Maho Girls Pretty Cures, to fight against them. Thus, Mirai is brought into a world of magic, where she and Riko must learn how to use magic in order to stop Dokuroxy.