Nakahara, also called the Ninja Master and the "Masked Ninja", is an evil ninja who is the leader of the Zeed crime syndicate and the main antagonist from Shinobi and it's two sequels, The Revenge of Shinobi and Shinobi III: Return of the Ninja Master. He attacks Joe Mushashi with his long hair and uses it as a boomerang also. In Shinobi III: Return of the Ninja Master, he has new attacks, such as shooting needles out of his long hair, and throwing bansho fans.
Obsessed with the idea of recreating the Sengoku era where the art of the ninja played a traditionally active role, he is the mastermind behind Zeed, the very organization he established in that quest. Always wearing a demon mask, he controls Zeed's operations secretly. In a bold move to gain political ground, he kidnaps the children of world leaders (as well as the children of the Oboro Clan in the original Japanese version). He commands his elite assassins and ruthless mercenaries to kill Joe Musashi for his interference in Zeed's plans.
The Masked Ninja secretly created Zeed in Japan, and under his orders, the children of the Oboro-ryu Ninja are taken hostage. His plan was to send Japan back into an era of war, and reignite the glory of ninjas everywhere. But he soon found his plans being quashed one after another by the young Oboro prodigy, Joe Musashi. Eventually the two would come face to face at the main headquarters. It is then that a violent struggle takes place. Despite the fact that their skills were almost similar, in the end, the masked Ninja was defeated. It would then be discovered that it was the Oboro ninja Nakahara, the man who taught Joe Musashi the Ninjutsu of the Oboro School, that was the wirepuller of the operation.
Nakahara was one of great skill, and the man who taught Joe Musashi Oboro-ryu Ninjutsu (朧流忍術 Rising Moon Style Shinobi Arts) , the Oboro clan shinobi art system of stealth and invisibility. However, he was irrevocably frustrated by the state the Ninja had submerged in modern times. Wishing to bring the Shinobi back into their glory days, where the shinobi played an active role of shaping Japan's history, Nakahara created the group Zeed to instigate this drastic change, going as far as to abduct the children of his own clan and make use of shinobi and killers to use for his ends, even going as far as to attempt the murder of his student to achieve his purpose.
- Nakahara's name is a reference to the Musashi-Nakahara Station. His name is meant to be a hint of his true identity as "Nakahara Musashi", Joe Musashi's father.
- Nakahara bears similarities to Braden, the Masked Ninja of Sho Kosugi's film Revenge of the Ninja, in that both were once trusted by the heroes of their respective story, but were involved in illicit businesses (one used Japanese dolls created by Sho's character Cho Osaki as a front for heroine deals, and the other secretly acted as leader of a terrorist organization to reinitiate a wartime.
- Nakahara also shows signs to Sho Kosugi's first acting role character Hasegawa in Enter the Ninja; an expert ninja who was frustrated because the Ninja had no active roles in the 20th century, and was part of the same clan that trained their rivals.