In modern Japan, ninja still operate in the shadows as covert agents of the state. Yodaka, an exceptionally skilled young shinobi with debilitating social anxiety, is assigned his most challenging mission yet: protect Aoi Mukai, a clumsy high school heiress targeted by fugitive ninja known as Nukenin. To complete his mission, Yodaka must enroll in her high school under the alias Yu Nozuki and blend in as a normal student, a task complicated by his complete inability to hold a conversation.

The story is set within a contemporary world where the Ninja Public Security Force (NPSF) manages these modern operatives, who often possess hereditary superhuman abilities called Kekkai. Yodaka is a unique case as he has no ninja lineage or Kekkai, relying purely on his natural talent. He is assigned to Squad 9, alongside Hibari (Kana Fujimiya), a skilled ninja tasked with becoming Aoi's best friend, and Umineko (Taki Utsumi), who is assigned to become her boyfriend. The squad takes orders from an enigmatic operator known only as Number Nine.

The early narrative arcs establish the mission and threats. The Introduction Arc and Miyake Arc see Yodaka foiling initial assassination attempts, including one by a seemingly bullied first-year student who is a renegade ninja. He unexpectedly sparks a genuine friendship with Aoi, who values his earnest awkwardness over the artificial politeness she usually receives. The Battle at the Mall Arc and School Camp Arc raise the stakes, the latter introducing a new mission where Yodaka must officially play the role of Aoi's boyfriend, forcing him to confront his growing romantic feelings for her.

As the series progresses, the scope widens. The Fugitive Ninja Hideout Infiltration Arc sees Squad 9 recruiting a new member, Suzume, and targeting an enemy warehouse. The subsequent Fort Port Arc relocates Aoi to a new fortress for her safety, and the Fugitive Ninja Mass Assault Arc features a large-scale enemy attack on the recovering squad. A notable antagonist introduced is Kawasemi, a fugitive ninja who mysteriously claims to be Aoi's older brother, despite official records stating she has no living relatives. The series continues to develop the mystery behind why Aoi is targeted and the internal conflicts within the NPSF, with later arcs such as the Kasasagi Arc and Infiltration Mission Arc building toward a larger confrontation.