In the seemingly perfect walled metropolis of No. 6, crime is nonexistent, medical care is advanced, and its citizens enjoy an unprecedented standard of living. Shion, a brilliant young man identified as an elite, lives a comfortable and sheltered life with his mother in the city's exclusive top tier. His assured future is thrown into chaos when, on the night of a violent typhoon, he discovers a wounded boy his own age, a fugitive from the city's correctional facility who gives his name only as Nezumi, meaning rat. Shion hides the injured escapee, treating his wounds, and helps him flee from the security forces. In return, Nezumi warns Shion that the city is not the paradise it pretends to be.

As punishment for aiding a fugitive, Shion is stripped of his elite status. Four years later, he lives a quieter, more ordinary life. When a mysterious and bizarre death occurs in his sector, Shion’s forensic instincts lead him to uncover a hidden conspiracy, and he is framed for the crime. Now a wanted man, Shion is forced to flee the only home he has ever known and ventures into the desolate and dangerous wasteland beyond the city walls. There, he is rescued by Nezumi, who has been living in a subterranean library and observing the city from the outside.

The narrative follows Shion and Nezumi as they work together to uncover the horrific secret upon which No. 6 was founded: the use of human experiments involving parasitic wasps designed to control the population, a program that has driven the city's creator mad. Their journey forces Shion to shed his naivety and confront the brutal reality of his former home, while Nezumi, who has dedicated his life to the destruction of No. 6, begins to see a future beyond revenge. Together, they navigate a dystopian world of surveillance, biological horror, and social collapse, finding their fates irrevocably linked as they strive to expose the truth and bring down the walls of the city that calls itself a utopia.