Athanasia de Alger Obelia, the only legitimate princess of the Obelian Empire, awakens memories of a previous life; from these, she sees a future where she dies at the hands of her father, Emperor Claude. While his gaze is full of affection for Athanasia's older sister, Jennette Margarita, he only regards Athanasia with indifference and leaves her desperately yearning for his love. To avert the fate that awaits her, the infant Athanasia resolves to escape the palace when she is older and, in the meantime, avoid meeting her father at all costs. However, their paths cross years before it was destined, and so young Athanasia finds herself at the mercy of Claude's seemingly mercurial whims. But the one emotion that she expects, apathy, is never present on his face. With a father who now considers her family, Athanasia strives to grow into a proper crown princess—but her grim vision may yet have ways to become true.

Yume Nijino has been accepted into Four Stars academy, home of the beautiful and talented S4 idol group. She and the other newcomers are determined to discover their talent, with a choice of specializing in beauty, singing, dancing, or drama. A tough road lies ahead of them, and they must rely on each other to overcome their weaknesses and develop their unique strengths. At the first-years' opening performances, Yume performs stellarly but faints and is unable to remember being on stage at all. Struggling to find her talent, she meets Rola Laura Sakuraba, and the two develop a friendly rivalry, working together to learn and improve. Though they have their differences, all the students share the same goal: to become the next S4 idol. But hard work and determination, along with teamwork, are needed if they want to join the elite S4.

Sunao Moriyama finds a strange but cute creature that he names Potemayo. Potemayo starts following him everywhere, usually riding on top of his head. His discovery becomes the center of attention in his class at school. Soon after, a similar creature appears, and is named Guchuko by one of Sunao's classmates. However, Guchuko doesn't seem to be as good-natured as Potemayo. (Source: ANN)

CG short specials of Flying Witch posted on the official YouTube channel of distributor VAP and later bundled with the Blu-ray and DVD volumes.