The story focuses on high school girl Nagisa Yukiai who lives in a seaside town. She has believed her grandmother's story that spirits dwell in words and they are called "kotodama" (word spirit). One day, she strays into a mini FM station that has not been used for years. As an impulse of the moment, she tries to talk like a DJ using the facility. But her voice accidentally broadcasted reaches someone she has never expected.

At last, the Sanzou Party has arrived in India. In this foreign land, where the anomaly's influence runs rampant, their battles only heighten in their violence. And also awaiting them is their tragic fate from 500 years ago— What will they find at the end of their long and treacherous journey?

In the previous series "Kite," a killer—Sawa—suddenly disappears after she avenges her parents' death, and no one knows where she is. Several years later, a figure dances airily on the dark side of a big city. She is an angel of death, killing her victim gracefully and disappearing. Monaka is a normal high school student, though this quiet and modest life has a darker side. An angel of death is Monaka's other persona.

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.