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.
The story is located in a colony "Industrial 7" in UC (Universal Century) 0096. It depicts an encounter of a 16 years old student Banagher Links and the pure white mobile suit "Unicorn Gundam", and also depicts the global basis war over the forbidden box "Laplace".