In a city built on the ashes of our world, what you don’t know…WILL kill you! In a near future world after the last great war, most of mankind now lives in a handful of city states. There, for the privileged elite, life should be perfect. But for young Shion, the only thing perfect has been the nightmare his life has become since letting a strange boy named Nezumi spend the night in his apartment. Banished to the outskirts of the city and stripped of all privileges for helping the mysterious stranger who has since disappeared, Shion now finds himself in even worse danger as his inquiry into a new series of mysterious deaths results in his being arrested on suspicion of murder! But even as Shion is being sent to the city’s Correctional Institute, the long missing Nezumi reappears to rescue him! Now, on the run, the two young men have only one chance at survival: uncover the mysterious secrets that lie at the sinister heart of City Number 6!
Shion is a gifted student leading a normal life: daydreaming in school and awkward moments with a close friend are the most trouble he finds himself in. All this changes when a chance encounter with a strange boy leads Shion down the wrong path.
By helping Rat that rainy night, Shion gets stripped of his elite privileges and thrown out of paradise. Meanwhile, a mysterious parasite is loose in the city, with Shion bearing witness to its destruction. Soon after, he is taken away without reason.
After a daring escape from No. 6, Shion learns that he has become infected. With Rat's help, they remove the parasite from his body. After analyzing the specimen, Shion comes to a horrible realization that threatens to destroy his former home and his friendship with Rat.
Inukashi blames Shion for Rat becoming soft over the years, which leads to a confrontation. Shion makes a decision that could greatly alter his life.
The death toll is slowly climbing. The mysterious parasites claim another victim, this time in the Twilight House, where Safu's grandmother lives. Rat suddenly faints during a theater performance; at the same time in No. 5, Safu also faints--but not before she hears a faint song in the wind...
After returning to No. 6 to gather her grandmother's belongings, Safu notices many strange things around her: objects that should be there are missing and everything seems out of place. Soon after, she is taken away by city officials.
Rat contracts Dogkeeper to gather information about the correctional facility. Meanwhile, Shion discovers Safu's old coat at a used clothing store. After piecing things together, Shion decides to make his way to the correctional facility himself, but not before a confrontation with Rat.
Shion and Rat head to the Western District in a mad dash to save Safu. On their way they meet up with an old man, known by Rat, and the first person to survive the parasite. Shion learns an unbelievable truth about Rat, as well as the real reason behind the creation of No. 6.
Holy Day is getting closer, and after gathering information about it, Rat, Shion, and Inukashi learn about a cleansing operation that will take place before Holy Day. Meanwhile, the rumble of tanks breaks up the city wide celebration in the streets of No. 6...
After being herded into the correctional facility along with the townsfolk of No. 6, Rat and Shion fight their way through the throngs and begin searching for Safu. Shion knows exactly where to turn as they make their way around the complex, which worries Rat. After fighting through many obstacles, they finally find Safu, but are horrified at the sight that lies before them.
The Holy Day is finally here, and chaos soon erupts around No. 6. Will Shion and Rat find a way to stop the coming wave of parasites? What will happen if they can't? What of Safu and the mysterious entity known as Elyurias? Find out in the exciting conclusion of No. 6!