There is no live-action TV series titled Watari the Ninja Boy. However, a live-action film based on the manga series Watari by Sanpei Shirato was released in 1966. The following synopsis is based on that film.

In sixteenth century Japan, the Iga province is divided by a bitter feud between two rival ninja clans, the Momochi and the Fujibayashi. This conflict is deliberately perpetuated by the clan leaders, who have created a secret Code of Death to keep the lower-ranking ninja, known as genin, divided and under control. To fill their ranks, children are kidnapped and forced to train in harsh camps scattered across the territory.

Into this turbulent landscape arrive two wandering ninja, a one-legged old man named Shikanme and his remarkably skilled young grandson, Watari. Watari, a boy who wields a small axe and possesses mystical ninja skills, quickly befriends a young ninja trainee named Kazura, who runs one of the training camps. Watari realizes that the existence of these camps keeps the supply of genin abundant and their lives expendable, and he asks Kazura to stop operating his camp.

Kazura has a sister named Tsuyuki, who wishes to marry her boyfriend, Kojiro. The only way for them to be together is to abandon the ninja life and become nukenin, or escapees. Clan leader Momochi offers them a chance to earn their freedom and marriage: they must infiltrate the fortress of Samidare and assassinate its lord. This mission, however, is a trap. Awaiting them are the Six Iga Ninjas, a group of color-coded warriors each possessing an outlandish superpower. Tsuyuki and Kojiro are both killed. Kazura, seeking to avenge his sister, follows her to the fortress and is captured.

Watari goes to Samidare fortress to rescue his friend. He battles the Six Iga Ninjas, using his supernatural abilities to defeat them one by one, including a technique called oboro no jyutsu which projects multiple images of himself. With the help of his grandfather Shikanme, Watari manages to eradicate the six ninjas. In a final act of vengeance, Kazura sneaks into the Fujibayashi fortress and blows it up, sacrificing himself.

Kojiro, who was thought to have died, is rescued by Shikanme. He uncovers the conspiracy at the heart of the clan war: Tateoka no Dojun and the vice-leader Otowa no Jyoto are revealed to be the same person. This mastermind, working with Momochi, deliberately split the Iga clan to make it easier for them to rule. Watari, having avenged his friends and exposed the truth behind the corrupt ninja code, continues his journey.