The game features new mechanics and changes. Such new features include ""Steel on Bone"", a new visual cinematic trick which allows players to cut through the body during a slow-motion sequence. The new Kunai Climb involves Ryu climbing onto certain walls with the use of his kunai, which he can use to attack enemies from above. In other situations the player has to be stealthy, as Ryu can now sneak up on an enemy and kill him with a single strike. Enemies speak while fighting and do not die quickly, and they suffer and scream in paiSome changes include the slide maneuver, which replaces the Reverse Wind Technique from the previous games. Ryu uses it to get through small passages as well as to attack enemies. The Ultimate Technique concept has slightly changed in the form of Ryu's cursed right arm known as the Grip of the Murder. When he kills a specific number of enemies his arm glows red. Then, the player can charge up for an ultimate attack that is fueled by absorbing nearby fallen bodies instead of essence.
Unlike past games, the HUD appears only when Ryu is engaged in battle, then fades out later. The Muramasa store is no longer present; Ryu gets different swords over the course of the game. He also has access to his shuriken and a high-tech bow; arrows for the bow are also improved as the game progresses. Both projectile weapons have infinite ammo. Items are virtually non-existent. The Dragon Statues that allowed Ryu to save and heal are replaced by a scripted Falcon who swoops down to Ryu's hand and saves at specific points in the level, restoring his health to full as well.
The Ninpo concept has been revamped. In the single-player mode, Ryu has access to only one Ninpo that transforms him into a giant dragon of fire. To activate it, the player must first defeat enemies to fill up a bar beneath the healthbar. Once it is full, the player can activate the Ninpo and kill all onscreen enemies at once, restoring Ryu's life in the process. The amount of health gained depends on how many enemies were left when the Ninpo was cast. In the multiplayer modes (both co-op and competitive), there are other Ninpo available, such as the Art of the Piercing Void.
The PlayStation 3 version of Ninja Gaiden 3 has an optional control scheme for the use of the PlayStation Move. This is to give players ""a new visceral edge when battling and slicing through their enemy's flesh and bone.