"Kage-jitsu!" centers on the life of a high school student, Kageyama Shinta, who becomes entangled in a world of espionage and deception after discovering his family's hidden legacy. The Kageyama family has a long history of serving as shadow operatives for a secret government agency, and Shinta is thrust into this clandestine world when his older brother, a seasoned operative, goes missing during a critical mission. Determined to uncover the truth, Shinta begins training under the guidance of his family's loyal retainer, a skilled operative named Ayame, who teaches him the art of stealth, combat, and intelligence gathering.

As Shinta delves deeper into the shadowy underworld, he uncovers a conspiracy involving rival factions vying for control of a powerful artifact known as the "Shadow Codex," said to grant its possessor unparalleled influence over global intelligence networks. Along the way, he forms alliances with other young operatives, each with their own motivations and secrets, including Rina, a tech-savvy hacker, and Tetsuo, a former rival turned reluctant ally. The group navigates a web of betrayals, shifting loyalties, and high-stakes missions, all while Shinta struggles to reconcile his ordinary high school life with his newfound responsibilities.

The narrative explores themes of identity, loyalty, and the moral ambiguities of espionage, as Shinta grapples with the ethical dilemmas posed by his missions and the sacrifices required to protect those he cares about. The series balances action-packed sequences with moments of introspection, revealing the personal struggles of its characters as they confront the consequences of their choices. Through its intricate plot and dynamic character interactions, "Kage-jitsu!" presents a compelling exploration of the hidden world of spies and the burdens carried by those who operate in the shadows.