Often considered untrustworthy, Japanese ninja were in fact unwaveringly loyal to their masters. But in modern-day Japan, high school student and self-proclaimed ninja Rekka Hanabishi finds it difficult to carry on their legacy, that is, until he saves a cute girl named Yanagi Sakoshita from a group of delinquents.

In the aftermath of the event, Rekka deems Yanagi worthy of being his master, swearing to protect her. As a sign of their trust, the two reveal their most valuable secrets to each other: Yanagi can quickly heal wounds, while Rekka can create fire with just a snap of his fingers. However, their dazzling exchange does not go unnoticed as a mysterious woman called Kage Houshi appears. She somehow knows about their powers and threatens them, claiming Rekka must be returned, for he is the only one who can kill her.

The pair hold their ground, but before things can escalate any further, Kage Houshi calmly leaves. Thinking the crisis is over, Rekka and Yanagi continue their daily lives, unaware that they are about to be dragged into a centuries-long ninja conspiracy with the lives of their friends and their own on the line.