No.6 unfolds in a world reshaped after a devastating war, where humanity survives inside six city-states that appear peaceful and flawless from the inside. In the seemingly perfect city-state No.6, Shion has grown up as an elite with every advantage, but a chance encounter with a mysterious boy named Nezumi changes the course of his life. Nezumi comes from the wasteland beyond the walls, a harsh world populated by those the city has cast aside. Although Shion knows Nezumi is a fugitive, he chooses to shelter him for the night and protect him, and that single act of defiance brings severe consequences: Shion and his mother lose their privileged status as elites and are relocated, while the polished surface of No.6 begins to crack.
Years later, Shion and Nezumi are drawn back together. The former elite and the boy on the run must face the true nature of the city they once knew, navigating a tense bond shaped by trust, betrayal, and survival. As they move toward the heart of No.6, their reunion sets off an adventure that gradually exposes the shattering secrets hidden behind its walls.