Six years following the events of Chaos:Head, a new string of deaths similar to the New-Gen murders have started up in the newly rebuilt Shibuya area. These incidents have taken the attention of a Highschooler: Takuru Miyashiro, and the newspaper club. Investigating the incidents of the present as well as their connection to the events of the New-Gen Crimes Takuru and his friends find themselves being pulled deeper into the incidents than they ever believed possible.
Yuu Haruna is the new boy in town and finds himself drawn to Fuuka. He discovers that they both have love for the same band and Yuu, who isn't too bad on bass, compliments Fuuka's raw singing voice. They decide to form a band together. Yuu wants to confess his growing feelings for Fuuka but his childhood friend and idol Koyuki still harbors feelings for Yuu.
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.