"Ninja Papa" centers around Taro Yamada, a former ninja who retires from his dangerous profession to lead a quiet life as a family man. After marrying his wife, Yuki, and becoming a father to their young daughter, Hana, Taro strives to leave his ninja past behind. However, his old life frequently intrudes on his new one, forcing him to balance his duties as a father with his exceptional ninja skills. The series blends comedy, action, and slice-of-life elements as Taro navigates the challenges of parenthood while occasionally confronting threats from his former ninja clan or rival factions.

The narrative explores Taro's efforts to protect his family while maintaining the facade of an ordinary life. His ninja training often comes in handy in unexpected ways, whether it’s using stealth to avoid nosy neighbors or employing combat techniques to fend off home intruders. Yuki, unaware of Taro’s ninja background, often finds his behavior peculiar but attributes it to his quirky personality. Hana, on the other hand, begins to notice her father’s unusual abilities, leading to humorous and heartwarming moments as Taro tries to explain his actions without revealing his secret.

Throughout the series, Taro faces various adversaries, including former colleagues who seek his help or enemies who want to settle old scores. These conflicts are interspersed with everyday family struggles, such as helping Hana with school projects or dealing with household chores. The juxtaposition of mundane family life with high-stakes ninja action creates a unique dynamic, highlighting Taro’s dual identity as both a devoted father and a skilled warrior.

The supporting cast includes Taro’s former ninja mentor, who occasionally provides guidance or complicates his life, and a rival ninja family that serves as both a threat and a source of comedic rivalry. The series also delves into Taro’s internal conflict as he grapples with his past and his desire to shield his family from the dangers of his former profession. Despite the challenges, Taro’s love for his family remains the driving force behind his actions, making "Ninja Papa" a story that balances humor, action, and heartfelt moments.