Natsume Tomoharu is a normal high-school student in every way with one exception: he's being followed by the ghost of his best friend, Misao. After moving into his brother's old house, Tomoharu expects to continue living his normal life but is one day left with a mysterious and locked briefcase without any instruction. At first he plans to leave it in storage; however, his house is soon invaded by multiple groups of people after the briefcase. Although still not knowing the purpose of the briefcase, Tomoharu and Misao attempt to escape with it. From there on, Tomoharu tries to learn the secrets behind the briefcase, the connections between it and Misao, and why it has the power to change the world.

Following the first season, Tomoharu is now faced with a dilemma: if he doesn't form a contract with an "akuma," he risks losing his dear friend Takatsuki. However, doing so would compromise his own existence as it would result in him and his ghost friend Misao becoming an Asura Cryin'—mankind's biggest threat, according to their school's presidents. To make the decision even harder, Tomoharu and Misao have recovered some of their past memories—memories of a world that they didn't even know existed.