"Ninja Girls" is a manga series set in a fictional historical Japan where ninja clans wield supernatural abilities. The story centers on Raizo, a young ninja from the Koga clan, who is tasked with retrieving a powerful artifact known as the "Dragon Jewel." This artifact is said to grant immense power to its wielder, and its theft threatens the balance of power among the ninja clans. Raizo's journey intertwines with three female ninja from rival clans: Ran, a skilled warrior from the Iga clan; Tenju, a mysterious and aloof ninja from the Fuma clan; and Sen, a cheerful and resourceful member of the Saiga clan. Each of these women has their own motivations for seeking the Dragon Jewel, and their paths cross with Raizo in unexpected ways.

As the narrative progresses, Raizo and the three ninja girls form an uneasy alliance to recover the Dragon Jewel and prevent it from falling into the hands of a shadowy organization seeking to exploit its power. The group faces numerous challenges, including rival ninja clans, treacherous landscapes, and their own conflicting loyalties. The story explores themes of trust, loyalty, and the consequences of power, as the characters grapple with their personal histories and the weight of their responsibilities.

The plot is driven by a mix of action, intrigue, and interpersonal dynamics, with each character contributing unique skills and perspectives to the mission. Raizo serves as the moral anchor of the group, often mediating tensions between the strong-willed Ran, the enigmatic Tenju, and the optimistic Sen. The series balances its action-packed sequences with moments of character development, revealing the backstories and motivations of the main cast. As the group grows closer, they must confront not only external threats but also their own inner conflicts, culminating in a climactic showdown that tests their resolve and unity.