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. [Written by MAL Rewrite]

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.

In a world where humans can have their wish granted via the Goddess Help Hotline, a human, Keiichi Morisato, summons the Goddess Belldandy by accident and jokes that she should stay with him forever. Unfortunately for him, his "wish" is granted. Suddenly, Keiichi is now living with this gorgeous woman all alone, causing him to be kicked out of the all-male dormitory he was staying in. But soon, after they find lodging in a Buddhist temple, Keiichi and Belldandy's relationship begins to blossom. Although they are both awkward and rather uncomfortable with one another at first, what awaits these two strangers could turn out to be an unexpected romance. [Written by MAL Rewrite]

One year after goddess Belldandy emerged from Keiichi Morisato's mirror and promised to stay with him forever, a new threat to their happiness emerges, one that could end the contract between Belldandy and Keiichi.