"Under Ninja" is set in a contemporary world where ninjas operate covertly within modern society, blending seamlessly into everyday life while carrying out clandestine missions. The narrative centers on Kuro Kumogakure, a high school student who leads a double life as a member of an underground ninja organization. The organization, known as the "Under Ninja Association," operates in the shadows, tasked with protecting national security and maintaining order through espionage, sabotage, and assassination. Despite their advanced skills and training, the ninjas must navigate the complexities of modern life, balancing their duties with personal struggles and societal expectations.

Kuro’s journey begins when he is assigned a critical mission to uncover and neutralize a rogue faction within the organization. This faction, led by a former elite ninja named Shiro Kage, seeks to destabilize the government and expose the existence of ninjas to the public. As Kuro delves deeper into the mission, he uncovers layers of corruption and betrayal within the association, forcing him to question his loyalty and the morality of his actions. Along the way, he forms alliances with other young ninjas, each with their own unique abilities and motivations, including Aoi Hoshino, a skilled infiltrator with a mysterious past, and Renji Tachibana, a combat specialist grappling with his own sense of duty.

The series explores themes of identity, loyalty, and the clash between tradition and modernity. Kuro’s dual life as a student and a ninja highlights the tension between his desire for a normal life and his commitment to his role as a protector. The plot is driven by a mix of high-stakes action, intricate political intrigue, and character-driven drama, as the protagonists face off against both external threats and internal conflicts. The narrative builds toward a climactic confrontation between Kuro and Shiro, where the fate of the Under Ninja Association and the balance of power within the ninja world hang in the balance. Through its blend of espionage, martial arts, and personal growth, "Under Ninja" offers a compelling exploration of the challenges faced by those who live in the shadows.