Tokyo is flooded with countless heroes — chōjin — during the time of "apotheosis." Their origin stories are all different. While some were altered by evil organizations, others came from space, magical worlds, or are fairies from ancient times or robots. But the Japanese government could not simply close its eyes as these superheroes ran rampant.
Eleven years after the introduction of internet-connected, augmented reality eyeglasses and visors, Yoko Okonogi moves with her family to Daikoku City, the technological center of the emerging half-virtual world. Yoko joins her grandmother's "investigation agency" comprised of children equipped with virtual tools and powerful metatags. She quickly crosses paths with Yoko Amasawa, an expert hacker of the virtual environment, as Amasawa relentlessly seeks to "unlock" the mystery of a computer virus that emerges from an inaccessible corrupted space.
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.
High school student Sota is watching the anime Elemental Symphony of Vogelchevalier when he suddenly finds himself drawn into it. When he returns to his world, the heroine of that series, the warrior-princess Selesia Uptiria, comes with him. They soon discover that this is not an isolated case, as several characters from anime, manga, and video games are being transported into what they call "the realm of the gods" by the mysterious girl Military Uniform Princess. Some Creations seek to meet their Creators, while others have more hostile purposes.