Kanzo Hattori, bekend als Nin, een van de laatste afstammelingen van de Iga-clan, wordt door zijn vader, grootmeester Hattori, naar Tokio gestuurd om zijn lot als ninja te vervullen. Maar in Tokio komt hij de jonge Kenichi tegen, die zijn leven redt. Nin zweert vervolgens trouw aan Kenichi en onderneemt een genadeloze strijd tegen de rivaliserende Koga-clan, om zijn jonge meester te beschermen...

Kanzo Hattori, an apprentice Ninja, leaves his home town of Iga for his final training. He must go to the city of Edo (Tokyo), and the first person he meets shall be his master, whom he must protect with his life, whilst upholding the ninja code. Also while in Edo, Hattori must find out why their rivals, the Koga Ninjas, are flourishing while the Iga Ninjas are dying out. Hattori's master is Kenichi, a 9 year old boy. Kenichi is an introvert and not very popular boy, so he never plays with the other children from school. Kenichi also has a secret crush on a young lady called Midori, yet he's too shy to speak to her. Though as he watches Hattori trying his best, he too begins to try. Meanwhile, people are being found unconscious, their bodies completely unmarked. All the victims have a tattoo (the Koga Ninja crest) and are found with a throwing knife lying close by.

Kanzo Hattori, dit Nin, l'un des derniers descendants du clan des Iga, est envoyé à Tokyo par son père, le grand maître Hattori, afin d'accomplir son destin de ninja. Mais à Tokyo, il croise la route du jeune Kenichi, qui lui sauve la vie. Nin prête alors allégeance à Kenichi et entreprend un combat sans merci contre le clan rival des Koga, pour protéger son jeune maître...