Kyuutarou ga Yattekita!

There's going to be a new student in Tesukayama School. To everyone surprise, that student is a girl, a ninja girl. Her grandfather died and she's the only one left in her ninja clan. Kyuutarou never been in a city before, since her sibling died when she was little, she's always live in the jungle alone with her grandfather and her dog. She never go to school, her grandfather is the one who taught her everything.

Motoi whose his father is also the school director is asked by his dad to take care of her and because of his family and Kyuutarou's family's relationship back in the shogunate era, Motoi's dad have to adopt her to live in Motoi's family resident. To complicate things more, there are ninja from other clans that try to hunt Kyuutarou down. What, more ninja? How the outcome of this chaotic story will be unfolded?