Similar to the first Game Gear Shinobi, The Silent Fury has Joe Musashi relying on his shuriken and sword skills, and Ninjutsu magic to rescue his ninja allies who each have their own unique abilities. The first four stages can be played in any order as players free a ninja in each one who then becomes playable. Every stage also has a crystal that can only be acquired by a specific ninja. Stages can be repeated and a password save feature allows the game to be saved after any of the stages leading up to the final stage against the Black Ninja.