"Kunoichi Sakuya" is a short-form anime series that blends historical ninja themes with comedic and supernatural elements. The story centers on Sakuya, a young kunoichi (female ninja) from the Iga clan, who is sent on a mission to assassinate Nobunaga Oda, a powerful warlord threatening her clan's survival. However, Sakuya's journey takes an unexpected turn when she discovers that Nobunaga has been reincarnated as a high school girl in modern-day Japan. This twist forces Sakuya to adapt to contemporary life while continuing her mission, leading to a series of humorous and chaotic situations.

The narrative explores Sakuya's struggles to reconcile her traditional ninja upbringing with the unfamiliar modern world. Her interactions with Nobunaga, now a cheerful and oblivious schoolgirl, create a dynamic filled with misunderstandings and comedic tension. Supporting characters include Sakuya's fellow ninja, who occasionally assist or complicate her mission, and various classmates who become entangled in her antics. The series balances its comedic tone with moments of action, as Sakuya employs her ninja skills to navigate both her mission and everyday challenges.

The plot unfolds episodically, with each episode presenting a new obstacle or scenario that highlights Sakuya's adaptability and resourcefulness. Themes of cultural clash, identity, and loyalty are woven into the story, as Sakuya grapples with her duty to her clan and her growing attachment to the modern world. The series maintains a lighthearted approach, using its historical and supernatural premise to deliver a blend of humor, action, and character-driven storytelling.