Ninja Gaiden III: The Ancient Ship of Doom is a side-scrolling platform game in which the player controls the player character Ryu Hayabusa as he investigates the events behind Irene Lew's death. In the game, Ryu can jump, hang, and climb up and down walls with the control pad; pressing the jump button while holding the control pad the direction away from the wall causes Ryu to spring off the wall. Ryu is also able to attack enemies with secondary weapons while on a wall by pressing the attack button.[21] A new feature introduced in Ninja Gaiden III is the ability for Ryu to hang overhead from pipes or ivy; he can swing up on top or drop from them, and as with walls, he can only attack enemies while hanging with secondary weapons.[7][22]
As with the previous Ninja Gaiden games, Ryu's physical strength is represented by a life meter on the top of the screen; it decreases when Ryu gets hit by enemies or other dangerous objects.[23] Throughout the levels, the player can find "Recovery Medicine" bottles that partially replenish Ryu's physical strength; as with all other items in the game, they are located in crystal balls that Ryu must slash to open.[24] The player loses a "life" when Ryu's life meter runs out, he falls into a pit, or if the timer runs out. The game ends when players lose all their lives,[23] but they can continue and resume play at the beginning of the Act in which they have lost all their lives. However, in the US version of Ninja Gaiden III, players only get five continues total before being required to restart the game from the beginning.[25][26]
Ryu can defeat enemies by attacking with his Dragon Sword or by using secondary weapons which consume Ryu's "ninja power"; such weapons include the following: "Windmill Throwing Stars" which move back and forth like boomerangs, "Fire Dragon Balls" which launch fireballs downward at an angle, the "Fire Wheel Art" which launches fireballs upward at an angle, the "Invincible Fire Wheel" that forms a series of rotating of fireballs around Ryu and destroys any enemy who comes into contact, and a new weapon in this series called the "Vacuum Wave Art" which hurls vacuum blades above and below Ryu simultaneously.[27][28] Players can collect red and blue capsules to refill Ryu's ninja power, and they can also collect "Scrolls of the spirit of the Dragon" to increase Ryu's maximum ninja power level. Another new item in Ninja Gaiden III is the "Dragon Spirit Sword" that increases Ryu range of his sword.[24] At the end of each Act is a boss which has its own life meter that decreases when damaged; Ryu can defeat the boss by completely depleting its life meter.[23] Ninja Gaiden III's first four bosses consist of the "bio-noids" – super-human creatures created and controlled by Foster to take over the world; they each represent the four elementals: earth, wind, fire, and water.[29][30]