It has been a month since Illya and Miyu became magical girls and sealed all of the Class Cards. Rin and Luvia have been forced to remain in Japan to clean up the aftermath, such as the now-unstable magic in the area's ley lines. While helping with the cleanup, the seal on Illya's mysterious innate magic goes berserk and she loses control of her transformation. By the time she has realized what happened, a mysterious girl who looks eerily like Illya appears, apparently bent on bringing destruction down on the original whose heart she seems to have spawned from, and making matters worse she holds the power of the Archer Class Card, with which Illya holds a special bond, within her body.
Miss Kobayashi is your average office worker who lives a boring life, alone in her small apartment–until she saves the life of a female dragon in distress. The dragon, named Tohru, has the ability to magically transform into an adorable human girl (albeit with horns and a long tail), who will do anything to pay off her debt of gratitude, whether Miss Kobayashi likes it or not.
Asahioka Branch School, a combined elementary and middle school in an isolated village, has only five students total, four girls and one boy. The girls are best friends, and pass the season with traditional activities like harvesting mountain herbs and fishing.