"Manga Mito Kōmon" is a historical comedy anime series based on the long-running Japanese jidaigeki (period drama) franchise "Mito Kōmon." The story is set during the Edo period and revolves around the retired daimyō Tokugawa Mitsukuni, also known as Mito Kōmon, who travels incognito across Japan with his loyal retainers, Sasaki Sukesaburō and Atsumi Kakunoshin. Disguised as a wealthy merchant, Mitsukuni investigates the lives of common people, uncovering corruption, injustice, and exploitation perpetrated by local officials and corrupt samurai.

The narrative structure is episodic, with each episode presenting a self-contained story. Mitsukuni and his retainers arrive in a new location, where they encounter individuals suffering under oppressive rule or facing personal hardships. Through their interactions, the trio gathers evidence of wrongdoing, often involving bribery, extortion, or abuse of power. The climax of each episode typically features a dramatic confrontation, during which Mitsukuni reveals his true identity by presenting an inro (a small decorative case) bearing the Tokugawa family crest. This revelation strikes fear into the hearts of the wrongdoers, who immediately surrender or face punishment. The series emphasizes themes of justice, humility, and the importance of leadership that serves the people.

Sasaki Sukesaburō and Atsumi Kakunoshin serve as both comic relief and skilled protectors, often engaging in humorous banter or physical confrontations with antagonists. Their loyalty to Mitsukuni is unwavering, and they play crucial roles in assisting him during his investigations. The dynamic between the three characters balances the serious tone of the injustices they uncover with lighthearted moments, making the series accessible to a wide audience.

The anime adapts the traditional "Mito Kōmon" formula with a comedic twist, incorporating exaggerated expressions, slapstick humor, and anachronistic elements that distinguish it from the more serious live-action adaptations. Despite its humorous approach, the series retains the core message of the original franchise: the importance of righteous leadership and the protection of the vulnerable. The episodic nature of the story allows for a variety of settings and characters, showcasing different aspects of Edo-period society while maintaining a consistent narrative framework centered on justice and moral integrity.