The story is set in early 17th-century Japan, immediately after the Battle of Sekigahara, as Tokugawa Ieyasu moves to consolidate power. Among his remaining enemies are the supporters of Toyotomi Hideyori, including the warlord Yukimura Sanada and his feared ninja clan. The elite warriors of this clan are known as sarutobi, legendary for their near-invincible combat skills. Tokugawa orders his right-hand man, Hanzo Hattori, commander of the Iga ninja, to hunt down every survivor of the Sanada faction, especially the sarutobi, whom he views as a grave threat.

One of the most formidable sarutobi is Daisuke Ozaru. He has a wife and a young son named Sasuke. After a fierce clash, Ozaru is wounded and barely escapes. Disguised as a traveling stranger, he returns home, but the hitmen pursuing him catch up and kill his wife. Little Sasuke witnesses his mother's death, unaware that the wounded traveler is his father. Ozaru cannot reveal his true identity, fearing for his son's safety. Father and son are forced to flee and wander across Japan, fleeing the relentless Iga ninja. During their journey, Ozaru secretly trains Sasuke in all the sarutobi techniques—stealth, combat, survival, and the harsh realities of a ninja's life. Along the road, they encounter a series of opponents: rival ninja, bounty hunters, and agents of Tokugawa.

The narrative follows this dangerous journey, focusing on Sasuke's gradual transformation from a traumatized child into a skilled and hardened warrior. Key story arcs include the initial tragedy and escape, the slow revelation of fatherhood under secrecy, the progressive mastery of sarutobi arts, and the constant threat of Hanzo Hattori's pursuit. The bond between father and son is tested by silence and danger, yet it forms the emotional core of the story. The manga won the 4th Kodansha Children's Manga Award in 1963 for its blend of historical action and drama.