After discovering the existence of demons in Tokyo, the original Cyborg crew led by Dr. Gilmore find themselves in conflict with Devilman, a strong demon believed to be in league with the war-profiteering terrorist organisation, Black Ghost. Meanwhile, a bigger threat emerges when Dr. Adams, a Black Ghost scientist unleashes his new line of high teen Cyborg models against 009 and his friends.

On the surface, Koudo Ikusei Senior High School is a utopia. The students enjoy an unparalleled amount of freedom, and it is ranked highly in Japan. However, the reality is less than ideal. Four classes, A through D, are ranked in order of merit, and only the top classes receive favorable treatment. Kiyotaka Ayanokouji is a student of Class D, where the school dumps its worst. There he meets the unsociable Suzune Horikita, who believes she was placed in Class D by mistake and desires to climb all the way to Class A, and the seemingly amicable class idol Kikyou Kushida, whose aim is to make as many friends as possible. While class membership is permanent, class rankings are not; students in lower ranked classes can rise in rankings if they score better than those in the top ones. Additionally, in Class D, there are no bars on what methods can be used to get ahead. In this cutthroat school, can they prevail against the odds and reach the top?

The story centers on an introverted high school student named Eiji Hoshimiya with a huge secret—he wished for the destruction of the world when he was younger. Fairies give certain people special powers called Orders, and what Order Users can do with their power depends on their wishes. Ten years after the Great Destruction, Eiji struggles to come to terms with his immense power.