In the backwater town of Bellforest lives a 14-year-old boy named Renton Thurston. He desires to leave his home behind and join the mercenary group known as Gekkostate, hoping to find some adventure to brighten up his mundane life. However, stuck between his grandfather's insistence to become a mechanic like him and the pressure of his deceased father's legacy, the only excitement Renton finds is in his pastime of riding the Trapar wave particles that are dispersed throughout the air, an activity akin to surfing. Everything changes when an unknown object crashes through Renton's garage, discovered to be a Light Finding Operation—a robot capable of riding the Trapar waves—specifically known as the Nirvash typeZERO. Its pilot is a young girl named Eureka, a member of the Gekkostate, who requests a tune-up for the Nirvash. Their meeting sparks the beginning of Renton's involvement with the Gekkostate as he takes off alongside Eureka as the co-pilot of the Nirvash.

It has been 10 years since Heaven's Gate appeared in South America and Hell's Gate appeared in Japan, veiling the once familiar night sky with an oppressive skyscape. Their purposes unknown, these Gates are spaces in which the very laws of physics are ignored. With the appearance of the Gates emerged Contractors, who, in exchange for their humanity, are granted supernatural abilities. In the Japanese city surrounding Hell's Gate, Section 4 Chief Misaki Kirihara finds herself at odds with an infamous Contractor codenamed Hei. Called "Black Reaper" in the underground world, Hei, like his associates, undertakes missions for the mysterious and ruthless Syndicate while slowly peeling back the dark layers covering a nefarious plot that threatens the very existence of Contractors. From the mind of Tensai Okamura comes a sci-fi thriller taking the form of a subtle exposé on a war in which political positions and justice have no sway—a war waged exclusively in the shadows.