Magic Knights are modern magic-users who fight with weapons converted from their souls. Ikki Kurogane goes to a school for these Magic Knights, but he is the "Failed Knight" or "Worst One" who is failing because he has no magical skills. However, one day, he is challenged to a duel by Stella, a foreign princess and the "Number One" student. In this duel, "the loser must be obedient for life."
In a time when magic is on the decline amid society, Atsuko Kagari is a cheerful girl who enters Luna Nova Academy in order to accomplish her dream of becoming a witch like her idol, Shiny Chariot. Shiny is a famous witch who disappeared from public view many years ago. On her way to school, Kagari meets the kind Lotte Yanson and the mischevious Sucy Manbavaran and the three become friends as they share a bedroom in campus. At the academy, Atsuko soon discovers she is in serious disadvantage compared to the other girls since she doesn`t come from a magical family and is required to learn the magical curriculum from scratch. Having found an item that once belonged to Chariot, Atsuko must discover how to activate and properly use the mysterious Shiny Rod as she hopes it might lead to finding out what has truly happened to her vanished idol.
Eruna Ichinomiya is a third-year junior high school student who has not decided on which high school to attend, and spends her days skipping school and playing games at home. One day, Eruna's eyes are captivated by a photo of Seisa Mikagura in a pamphlet for Mikagura Private Academy, given to her by her cousin, Shigure Ninomiya. Feeling that it is fate, Eruna decides to attend Mikagura Academy. However, Eruna discovers that Mikagura Academy is a school where only cultural clubs exist, and that it has an intense battle system where students with special powers must fight each other as representatives of their own clubs.