Tokyo is a hub of information technology companies in a future world, where biotechnology is significantly advanced. Access to data encryption is critical in order to protect valuable corporate and financial data from organized crime. A quasi-governmental organization, known as the System, controls access to legal encryption technologies and methods. System operatives known as Calcutecs serve as living encryption devices, using bio-algorithms hidden in their subconscious neural circuitry to securely encrypt data. An organized crime network known as the Factory opposes the System at every stage. One man has developed the next step in encryption technology and made some advances within the System's developmental laboratories, but only at a high cost. Most operatives mentally modified to perform the new process die within a few months; only one has survived. Embroiled in moral quandary, the scientist leaves the System but pursues his research goals independently. He surreptitiously involves the sole surviving Calcutec in his scientific investigations and through a miscalculation in his ability to control his experiments realizes he has consigned the man to death.

The narrative structure of the novel is atypical as it presents two distinct narrative threads which alternate between odd-numbered and even-numbered chapters. In fact, the novel can be read as two independent novels. First, there is the Hard-Boiled Wonderland, encompassing the odd-numbered chapters. Then, there is The End of the World, encompassing the even-numbered chapters. Hard-Boiled Wonderland, set in a gritty urban environment, tells the story of an unnamed Narrator as he slowly realizes his unwitting involvement in biotechnology experiments on his own mind and consciousness. He meets several characters through the course of the novel and learns he has been the subject of secret experimentation which will, ultimately, result in the death of his consciousness and his physical body. He is unusually muted in his response. Rather than trying to avoid his impending demise, he seeks to enjoy a final day of satisfying activities.

The End of the World is contrarily set in a dreamy other world where inhabitants perform menial tasks without ambition and execute the routine of their nearly medieval lives with exactness lacking in emotion. The narrative focuses on the experiences of a man, a Dreamreader, confused and out of place, as he enters an enclosed town called End of the World. Upon entering the town, the Dreamreader's shadow physically is cut away from him and thereafter leads a separate existence as an independent character. The Dreamreader explores the town in great detail, meets its inhabitants and tries to develop relationships with them. He eventually learns, however, that they are basically mindless automatons, who are unable to feel emotion or develop deep bonds of friendship. Meanwhile, his shadow has devised an escape plan. At the conclusion of the second narrative thread, the Dreamreader helps his shadow to escape but chooses to remain behind and continue his strange existence within the town.

In reality, the second narrative is a gradually-developing altered state of consciousness of the first narrative's protagonist. The town is the edited and programmed alternative mental reality created by the System's scientist and implanted into the narrator's mind. The gradual fusion of his consciousness with this altered consciousness results in the mental deterioration of the narrator and, ultimately, his death.