Life in the futuristic city No. 6 cannot get any better, particularly for the top-ranking student, Shion. Since the age of two, he has lived peacefully in his district with a bright future ahead. However, on the night of his 12th birthday, his perfect life changed forever. An unknown injured boy of his age, standing before his room's open window, strangles him. Despite the danger, Shion insists on tending to the stranger's wounds rather than setting him free. The intruder, a fugitive named Nezumi, reveals to Shion that the city is not as immaculate as it appears. The following day, Nezumi leaves without a trace, and the incident strips Shion and his mother of their elite status. Four years after that fateful stormy night, unimaginable events transpire, causing Shion to doubt the authorities sworn to protect his home. When he is falsely held responsible for these occurrences, he once again crosses paths with Nezumi, who spares him from permanent captivity. Now, as wanted criminals, Shion and Nezumi have no choice but to explore and unveil the pretentious facade of No. 6.