Mirai Asahina, a thirteen-year-old girl who is excited by various things, goes with her stuffed bear, Mofurun, to investigate a mysterious object that fell from the sky. There, she meets a young magician named Liko who is searching for something known as the Linkle Stone Emerald. When dark servants of Dokuroxy come seeking the Linkle Stone Emerald, Mirai and Liko join hands with Mofurun and transform into the legendary magicians known as the Pretty Cures to fight against them. Thus, Mirai joins Liko in attending Magic School, where they must learn how to use magic while also fighting off Dokuroxy's minions.
After being miraculously reunited a few years later, Mirai and the others begin to take steps towards their futures in their respective worlds. Mirai is a college student in the Magicless World. Liko, who returned to the Magic World, is a teacher at the Magic School. Mofurun, as always, is at Mirai's side. Ha-chan exists far away, watching over the world.
However, a new disaster threatening the Magic and Magicless worlds has appeared...
Due to signs of the coming disaster, Mirai and Liko reunite for the first time in months.
While attempting to resist this mysterious enemy, they both come face to face with not only their past, but their future.
With the magical words "Cure Up RaPaPa!", their exciting tale is once again set into motion!