The Shadow Master is the Leader of ZEED and ruler of ZEED's massive empire. Always wearing a crimson Oni mask with the ZEED emblem, the Shadow Master controls ZEED's ninja forces and army, ruling the world with an iron fist.
The Shadow Master is a manipulative mastermind. For years he has led the ZEED army in secret, keeping his identity a mystery to only his most faithful subordinates. He doesn't tolerate failure, and is as ruthless as he is cunning. Occasionally he'll appear just to taunt Jiro, when his loyalty is to a power even higher than his own.
During the Keicho Era, the Shadow Master served as one of the lords of the ZEED Ninja Group. The ZEED forces defied the will of the Emperor, and Jiro was tasked with their destruction. Realizing that all was lost if Jiro saw his face, the ZEED Ninja bought him time to escape before Jiro could spot him.
Upon learning that Jiro still lives, the Shadow Master sends his forces to eliminate him. After nearly killing Sarah only to be stopped by Jiro, his identity is revealed upon his mask's being broken by a stray bullet from Sarah. He is then defeated by Jiro, but Jiro spares him out of respect for the man he called master, but the Shadow Master strikes the ships controls and dies in the crash.
- The battle with Shadow Master is reminiscent to the Final Boss of Revenge of Shinobi and the original Shinobi Arcade game; being that the boss attacks with his hair as a weapon, and the fact that the enemy is the man who taught the protagonist Ninjutsu from the same clan.
- At the beginning of the secret mission, the Shadow Master lies unmasked and dead from the crash of the space ship.