Kumogakure Kuro is a modern day ninja, but that doesn't mean his life is exciting. Bereft of any missions for a long time, he's an underachiever whiling away his days in obscurity, until he receives a special delivery.

Kuro's been assigned a mission to infiltrate Kodan High School, but while waiting for his enrollment to finish, he's tasked with confronting a mysterious assailant with a very particular target.

Kuro sets a trap and catches a high school boy named Eita. Upon returning home Eita encounters Junna who wants to borrow his drone. Eita agrees to let her if she can find the blond foreigner.

Kuro goes to take his placement tests for school where he meets Noguchi who is there for extra lessons. After the tests Kuro and Noguchi walk home together and Kuro introduces her to Kawado.

After coming to Eita's aid in a conflict with some school delinquents, Kuro makes his way to the school's boiler room where he confronts the director. Later on the defeated Noheji requests Kuro's aid in fighting some students from Yankii High.

After the lady at the convenience store is attacked by an invisible individual and killed, an Emergency Shinobi Notice is sent out and an investigation is launched in an effort to ascertain the identity of the culprit.

Kuro scares Noguchi after sneaking into her room to tell her not to go to school. Yoshida recounts his history of being a writer and how it was influenced by various ninja.

Ranran finishes her analysis of the UN's invisibility suit and sends her findings to Kato. Saruta begins his attack on the school and starts cutting down the students and faculty.

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Hibi loses his fight to Yamada and now it's time for Kuro to step up to the plate. Noguchi encounters Sato and Suzuki while following orders from the Director and he leads them into a secret underground facility formerly run by the Japanese army.

The battles at the schools reach their climax. When all is said and done who will be left standing and what will be the outcome?