A gate appears in Tokyo's Ginza district sometime in the 21st century. From the gate pours out monsters, knights from middle-age Europe, and other fantasy-like beings, and they kill many of the citizens of Tokyo. This event is known as the Ginza Incident. The government sends a small group of soldiers from the Japanese Self-Defense Forces to the alternate world beyond the gate. Led by otaku soldier Yōji, they find that the villages in the world are being attacked by a dragon. An elf girl who is a survivor from the dragon's rampage joins the group in their travels across the dangerous new world.
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.
In a world where dead people turn into books and are stored in the Bantorra Library where anyone who reads a book can learn their past. Bantorra Library is maintained by Armed Librarians who wield psychic powers and their enemy is a religious society known as Sindeki Kyōdan.