Born of legendary origins, the young Madara has grown up in obscurity as an apprentice blacksmith. An encounter with the demonic Mouki reveals his destiny, and catapults him into the middle of a mystic quest. Madara fights for revenge with the help of freedom fighters, magical swords and Kirin, the master of the Majin. His goal is to defeat his brother and then overthrow his father, the despotic Miroku.

In the year 2010 AD, Hyper Hurricanes born concurrently all over the world caused severe damage. Five billion people lost their lives, decreasing the world's population to 3 billion. Existing economies and military were wiped out. Countries were frozen under solid ice, plains sank beneath seas, the world was changed dramatically. Human civilization enters a chaotic era. Poverty flourished outside of these economic zones and slums were widespread. The ruling class called themselves Logos and maintained their position by force of arms. They call the poor Revenus, who are exiled to live outside the special economic areas. Time has passed since then. Katsuragi Jo and Tsurasawa Jin, escape from Phantom, a force organized to watch Revenus and to suppress renegade elements of the Logos, taking with them a mysterious girl, Nobuto Sana. There are many who are interested in her, all with their own reasons.

It all begins with the story that was left untold—the earth-shattering incident where Renton's father disappeared. With the mysterious pilot Eureka by his side, only Adroc Thurston could undo his own mistake, sparking the event that changed everything and earned him the title of a hero. Now, ten years later, Eureka lies in critical condition as Renton leaves the crew of the Gekko. But when he finds himself in the care of his father's old friends, he has a choice to make. Either stay with the loving family he's always wanted, or earn the love he seeks.

On a sunny July day in the 41st year of the Shinka Era, Jirou Hitoyoshi is tasked with covertly listening in on a secret meeting between a top government scientist and an industrial spy. However, his cover is blown, and the spy reveals himself to be an alien in disguise. Amidst the ensuing chaos, Jirou enlists the aid of cafe waitress and magical girl Kikko Hoshino, one of many "superhumans" who blend into society and secretly protect humanity from extraterrestrial threats. As a member of the government agency known as the Super Population Research Laboratory, Jirou has the dual task of protecting superhumans that defend humanity and disposing of any deemed too dangerous to live. Having proven herself a worthy ally, Kikko is invited to join the agency as its newest recruit. Fast forward five years: disapproval and distaste for superhumans are now commonplace in Tokyo. From government corruption and conflicting ideas of justice, to the morality of superhuman rights, the relationship between humans and the supernatural minority balances precariously in a world pervaded by whispers of unrest and unease. Under mysterious circumstances, Jirou has betrayed the agency, and is now a fugitive on the run. As he skulks through the rainy back alleys of Shinjuku, he is pursued by the very same superhumans that he himself once recruited.