Life in the futuristic city No. 6 cannot get any better, especially for top-ranking student, Shion. Ever since he was two years old, he has lived peacefully in his district with a bright future ahead of him. However, on the night of his 12th birthday, his perfect life changed forever.

Standing in front of his room's open window, an unknown injured boy of his age strangles him. Despite being in danger, he insists on tending to the stranger's wounds instead of setting him free. The intruder, a fugitive by the name of Nezumi, reveals to Shion that the city is not as immaculate as it seems. The following day, Nezumi leaves without a trace, and the incident renders Shion and his mother void of their elite status.

Four years after that fateful stormy night, the most 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.