In the feudal era of Japan, Ogami Itto serves as the Shogunate’s chief executioner, a position of immense authority and trust. His life is shattered when the treacherous Yagyu clan frames him for treason to steal his office. Following this dishonor, his wife Azami is brutally murdered and his household is destroyed, leaving only his infant son, Daigoro, alive. Disgraced and stripped of his rank, Itto becomes a ronin and takes the path of the assassin for hire. He places his young son in a baby cart, which often carries weapons and his son's toys, and the two wander the countryside as the infamous pair known as Lone Wolf and Cub.

The central conflict is twofold: Itto must survive as a mercenary, accepting contracts to kill targets ranging from corrupt officials to rival clansmen, while relentlessly pursuing revenge against the Yagyu clan who destroyed his life. Each episode typically follows a formula where Itto and Daigoro arrive in a new town or region, become entangled with local lords, yakuza, or desperate commoners, and Itto is hired to carry out an assassination. These episodic assignments often explore themes of honor, duty, and the high cost of violence, with Itto’s reputation alone sometimes enough to intimidate opponents.

Throughout the series, the Yagyu clan, led by Lord Retsudo, continually dispatches assassins, ninja, and master swordsmen to eliminate Itto, fearing his quest for vengeance. Notable narrative arcs include encounters with rival samurai such as Gunbei Yagyu and Asaemon the Beheader, as well as storylines where Daigoro is separated from his father and must survive on his own, demonstrating the harsh education Itto is giving his son. The series blends graphic sword violence with a contemplative tone, showing the bond between father and son as they walk what is called the Assassin’s Road, moving from one deadly confrontation to the next across the Japanese countryside.