"Jubei-Chan The Ninja Girl - Secret of the Lovely Eyepatch" is a 24-episode anime series that blends comedy, action, and supernatural elements. The story centers on Jiyu Nanohana, a high school girl who leads an ordinary life until she encounters a mysterious man named Koinosuke Odagiri. Odagiri reveals that Jiyu is the reincarnation of Yagyu Jubei, a legendary samurai from the Edo period. He presents her with the Lovely Eyepatch, a magical artifact that grants her the combat skills and strength of her predecessor when worn.

Jiyu reluctantly accepts the eyepatch and the responsibility that comes with it, as she is tasked with protecting the Yagyu Scroll, a powerful artifact sought by the Yagyu clan's ancient enemies. These enemies, led by the villainous Freesia Yagyu, aim to use the scroll's power for their own nefarious purposes. Freesia and her followers, known as the Yagyu Seven, repeatedly challenge Jiyu, forcing her to balance her newfound ninja duties with her everyday life as a teenager.

Throughout the series, Jiyu faces numerous battles against the Yagyu Seven, each encounter testing her growing skills and resolve. She is aided by Odagiri, who serves as her mentor and protector, and her best friend, Miyu, who provides emotional support and comic relief. As the story progresses, Jiyu learns more about her connection to Yagyu Jubei and the true nature of the Lovely Eyepatch, which holds a deeper significance than initially revealed.

The narrative explores themes of identity, legacy, and the clash between modern life and ancient traditions. Jiyu's journey is marked by her struggle to reconcile her ordinary teenage experiences with the extraordinary demands of her ninja heritage. The series combines lighthearted humor with moments of intense action and emotional depth, creating a dynamic and engaging storyline. By the conclusion, Jiyu's growth as both a warrior and an individual is evident, as she embraces her dual identity and confronts the challenges posed by her enemies with determination and courage.