The ruthless Minister Honest exploits the ignorance of a new young Emperor and deviously rules the country from the shadows with twisted morals and no regard for human life. As a result of this, an epidemic of crime and corruption has spread throughout the country's capital city, and a state of society ensues where the privileged have absolute domination over the lesser.

However, there exists an organization to combat this rife abuse of power: Night Raid, a secret division of the oppositionary Revolutionary Army. It is composed of a small team of ruthless assassins who murder all those who partake in or turn a blind eye to the Empire's outrageous wrongdoings.

Tatsumi is a naïve, sword-wielding young man on a journey to save his impoverished village. Soon, he witnesses the bloody horrors and cruelty of the capital firsthand. Overcome with hatred, Tatsumi is swayed by Night Raid's profound cause and decides to join them, embarking on a painful and dangerous mission to exact revenge on Minister Honest. Tatsumi gains many invaluable experiences as he unravels the ethics of conflicting ideologies, life and death, all while working toward the restoration of a humane world.