Mitokomon is a fictionalized portrayal of Tokugawa Mitsukuni, the historical vice-shōgun and retired daimyō of the Mito Domain. Traveling incognito across Japan disguised as a commoner, he observes local living conditions and investigates corruption among officials. His mission is to ensure justice and report findings to central authorities.

He journeys with consistent companions: Suke, a master swordsman; Kaku, a strongman possessing exceptional physical prowess; his grandson Sutemaru; and a dog named Dombee. A girl named Yuki occasionally joins the group. These companions assist in investigations and confrontations.

Mitokomon's methodology follows a recurring pattern: he arrives in a village, witnesses injustices or mysteries, conducts covert investigations, and confronts perpetrators. Conflicts typically culminate in physical altercations resolved by Suke and Kaku subduing minions. Mitokomon then reveals his identity by presenting a distinctive inrō case, prompting the surrender of wrongdoers. He delivers judgments, punishes villains, and offers guidance to affected communities.

Visually, he possesses traditional Japanese features, including a white beard. He wears lavish clothing befitting a wealthy retiree and carries a walking staff that doubles as a defensive weapon, maintaining his incognito guise as a merchant.