Nakahara (in Japanese: 中原), also known as the Masked Ninja (in Japanese: 仮面忍者),, 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.
Originally a member of the Oboro Ninja Clan, Nakahara was a respected member of the Oboro-ryu's top Master Ninja. During this time he was the instructor and confidant to his young apprentice Joe Musashi. Initially the weakest in his class, Joe's tenacity earned Nakahara's admiration, and under Nakahara's guidance, Joe became the star shinobi expert of the Oboro clan as a teenager much to Nakahara's delight. However, as time went on, Nakahara became increasingly frustrated by the lack of Ninja activity, as the times of peace made it nearly impossible for ninja across Japan to have actual missions like his ancestors did in the past. His frustration reached a boiling point, and he decided to leave the clan in pursuit of his own group.
Years passed and Nakahara, through connections and manipulations of the criminal elements from disgruntled soldiers and thugs to rogue ninja set his new organization in motion. As the criminal mastermind the Masked Ninja, Nakahara secretly created the Zeed Crime Syndicate in Japan as 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.
Under his orders, the children of the Oboro shinobi and world leaders were taken hostage. His plan was to ignite a vicious civil war, and train the Oboro children as Zeed's obedient and powerful soldiers in a new feudal era, where the ninja could at long last have a chance at glory. 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.
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.
- Ninjutsu Master- As a master of the Shinobi Arts, Nakahara was able to use various forms of stealth and mystic techniques, from the techniques he taught to Joe Musashi (which ironically became his downfall) to various forms of combat.
- Sorcery and Necromancy- Nakahara possessed a knowledge of forbidden arts, including the ability to reanimate dead ninja zombies. Thanks to this he can almost indefinitely summon minions from the spirit realm to attack Joe from a Karasu-Tengu to hopping Oni.
- 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.
- Due to his mastery of dark arts as well as Ninjutsu, Nakahara is the first villain in Shinobi History to actually manipulate the dead.