Nakahara (in Japanese: 中原), also known as the Masked Ninja, is the final boss of Shinobi and the main antagonist of the game. A ninja boss character who uses the same kinds of Ninjutsu as Joe Musashi himself, this coupled with his penchant for constant jumping around making him the trickiest boss of the game.
The Masked Ninja is the mastermind behind the criminal organization of Zeed. 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 then sends his top killers and mercenaries to kill Joe Musashi and prevent his interference.
A mysterious criminal mastermind, the Masked Ninja secretly created the Zeed Crime Syndicate in Japan. A master of both combat and the mystic arts, he lords over the syndicate as the leader of the Ring of Five. Always wearing a Hannya mask, his identity had been speculated upon with many rumors. One prevailing theory is that he was an Oboro clan ninja gone rogue, but had yet to be confirmed.
Under his orders, the children of the Oboro shinobi and world leaders were taken hostage. However, things weren't going to plan as 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 the rumor was true; the leader of Zeed was the Oboro ninja traitor Nakahara; the man who taught Joe Musashi the Ninjutsu of the Oboro School, that was the wirepuller of the operation. It is revealed that Nakahara set up the Zeed due to being frustrated and obsessed with the idea of recreating the Sengoku Era where Ninja played a traditionally active role.
Nakahara was a man of great skill, and taught Joe Musashi Oboro-ryu Ninjutsu (朧流忍術 Oboro School of Shinobi Arts) , the Oboro village's shinobi art system of stealth and invisibility. However, he was irrevocably frustrated by the state the Ninja had fallen on 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 Zeed to instigate this drastic change, going as far as to abduct the children of his own clan and make use of disgruntled shinobi and killers to use for his ends, even going as far as to attempt the murder of his student to achieve his goal.
- 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 group to reinitiate the Era of War.
- 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.