Due to being an interquel between Ninja Gaiden and Ninja Gaiden II: The Dark Sword of Chaos, Late Arrival Spoilers for both games will be left unmarked. You Have Been Warned!
CIA Analyst Irene Lew, on assignment for a mission called "Cardinal" is attacked and seemingly killed by a man resembling Ryu Hayabusa. Knowing he had no involvement in her death and demanding answers, Ryu stakes out to find out what Irene was investigating and find out what really happened to Irene.
While the game was still insanely popular, the game was criticized for its increased difficulty in America.
Also notable for the Atari Lynx port being the last official game released for the system.
Provides examples of:
- Action Girl: Irene gets this, having been able to pull of a Faking the Dead to find her answers and ending firing a machine gun into the gut of a Bio-Noid.
- Beat Them at Their Own Game: A villainous version. Most of the bosses in The Ancient Ship of Doom use Ryu's Ninja Arts such as the Windmill Throwing Star or mass-fire versions of the Art of the Fire Wheel.
- Big Bad Wannabe: Foster puts himself in the Big Bad position, but he's only a pawn in Clancy's game and is unceremoniously ripped to shreds trying to enter the Life Energy realm.
- Clear My Name: The first half of the game involves Ryu doing this, wanting to know what the hell happened to Irene and who actually killed her.
- Conspicuous Electric Obstacle: Level 7-2 has electric hazards in form of electric beams.
- Difficulty by Region: The NES version of III has no password feature, limited continues, fewer checkpoints and stronger enemies than its Famicom counterpart.
- Doppelgänger: Partway through the game, Ryu runs into the person who killed Irene, claiming that he was created to be like him, but even stronger. He's revealed to be a Bio-Noid himself.
- Evil All Along: Clancy is the true mastermind of the events as he manipulated Ryu, Irene, and Foster into being his pawns.
- Good Cannot Comprehend Evil: Discussed at the end of the third game. Irene cannot comprehend evil, but Ryu can:Irene: I'll never understand why people make and pursue evil plans until they wind up dead.Ryu: Humans are always striving to achieve. All of creatures on earth, in all worlds, can never be just a part of someone's plans. Fortunately, mankind is never foolish enough to wipe itself out to achieve some ambitions.
- Interquel: The Ancient Ship of Doom takes place after the events of the first NES Ninja Gaiden, but before The Dark Sword of Chaos, which is why Ryu still possesses the Dragon Sword, despite having lost it at the end. The Japanese manual makes the game's setting clear, but the American manual only implies it subtly.After Ryu's victorious duel with Jaquio, Ashtar returned to the bowels of darkness and bided his time. But another evil creature was already on its way as another adventure awaits the unsuspecting Ryu Hayabusa...
- Mutually Exclusive Power-Ups: Weapon pickups from the background destroyables will replace the currently equipped one. However, this installment is the first that shows the new weapon hidden in said destroyable, removing potential guesswork.
- Quicksand Sucks: Quicksand makes appearance as an obstacle.
- Race Against the Clock: In Act 7 of The Ancient Ship of Doom, should you make it to the Final Boss without dying, you will notice the timer is very close to zero once you reach the end.
- Rock Beats Laser: Throughout The Ancient Ship of Doom, instead of heading into a hellish dimension to battle demonic creatures like its preceding games, Ryu faces a high-tech robotic army at (mostly) artificial environments, culminating with a battle within an alien ship against a laser-equipped Humongous Mecha.
- Oh, Crap!: At the Final Boss of The Ancient Ship of Doom, Ryu instead stutters out the villain's name upon seeing its monstrous form.
- Spike Balls of Doom: Rolling spiky balls appear as a fairly common hazard that needs to be avoided.
- Spikes of Doom: Tall Spikes do make an appearance. These periodically retract, allowing the player some time to go through areas.
- Warm-Up Boss: The Mantis Warrior from Stage 1 continues the tradition of trivially easy bosses, as he moves slowly and has a single ground-based attack that can easily be avoided. The only difference setting him apart from the Barbarian and Dando is that he can block.
- What Happened to the Mouse?: The game answers what happened to Foster following the events of the first game.
