The series is set 150 years after humanity lost half of the planet due to a mysterious "black fog." To contain the "black fog," 3,000-meter-tall (about 10,000-feel-tall) walls were erected to split the world, and the half of the human population that survived now live in cities called "Arks."

Shidou Enishi, one of the few Japanese survivors, runs a detective agency on the ninth ark. While pursuing a male suspect in a burglary, he learns of a massive conspiracy, one that may be tied to the Rivigarudo syndrome that is mutating its victims into something inhuman.