The third in the Last Ninja series sees you as Armakuni, the Last Ninja. He is drawn again into a battle with evil Shogun Kunitoki. The battle will take place among the temples of Tibet, the source of the Last Ninja's mystical strength. The Shogun intends to corrupt these Buddhist temples, to destroy the source of power for Armakuni and his emerging Ninja brotherhood. Armakuni must stop the Shogun's evil scheme.
The game retains the mix of martial arts combat (hand-to-hand and with various weapons), puzzles involving various objects you find on your way, and navigating your way around obstacles. However, it also introduces Bushido, necessary to complete each level. Bushido is earned by fighting honorably, by fighting enemies with the same weapon as them or in hand-to-hand combat, and not fleeing from a battle. The levels correspond to the elements that combine to make up a Ninja's power, Earth, Water, Wind, Fire and Void.