Ninja Gaiden III: The Ancient Ship of Doom - Plot

Plot

Ninja Gaiden III: The Ancient Ship of Doom takes place between the events of the original Ninja Gaiden and Ninja Gaiden II: The Dark Sword of Chaos. The story opens with Irene Lew, one of the protagonists in the first two Ninja Gaiden titles, an agent for the Central Intelligence Agency on a mission called "Cardinal". She gets chased to the edge of a cliff by a man who looks like Ryu Hayabusa, when the edge gives way, and Irene falls in the water to her death. Ryu is accused of Irene's murder but says it was not him, that it was somebody else who looked like him who tried to frame him. He first investigates a laboratory that Irene was investigating. After going through the laboratory, a mysterious man appears and tells Ryu to go the Castle Rock fortress, where he will give Ryu more information about Irene when he gets there.

On his way to the outer limits of Castle Rock fortress, Ryu encounters Foster, who was the head of the CIA's Special Auxiliary Unit in the first Ninja Gaiden game, via a video image. After saying that nobody has ever made it through the fortress' defenses alive, Ryu inquires out the whereabouts of Irene, in which Foster replies: "I don't know what you're talking about." Ryu vows to push on, Upon reaching the foundation of Castle Rock fortress, Ryu encounters his "original", or a person designed to look like Ryu, and finds out that is was he who killed Irene. They both thrust themselves at each other, and afterwards look-alike tells Ryu that he has gained all of his powers. The look-alike flees, saying that Foster ordered him not to eliminate Ryu quite yet.

When Ryu reaches Castle Rock fortress, he encounters the stranger whom he met after his trip to the laboratory, who reveals his name as Clancy. He tells Ryu about a project he and Foster have been working on called the "Biohazard plan". Clancy says that he can no longer work with Foster. He said Foster was designing creatures called "bio-noids" – transformed superhumans that are infused with "life energy" that flows from an interdimensional rift that appeared after the demon from the first Ninja Gaiden game was defeated. He explained that this rift appeared at the site of the Castle Rock ruins, in which Foster rebuilt in order to harness this power. Clancy reveals that it was a bio-noid that killed Irene, and that Foster controls the bio-noids; he pleas to Ryu to stop Foster. After making his way into the fortress, he encounters Foster and the look-alike. Foster vows to eliminate Ryu and use the life energy from the rift and Ryu's secrets of the Dragon Clan to make him into an all-powerful bio-noid. Just as Foster and the look-alike advance on Ryu, Irene appears, to the amazement of both Ryu and Foster, and is armed with a machine gun; she was working with the army with regards to Foster's plan. The look-alike then transmutes into a bio-noid, which Ryu defeats.

After the defeat of the look-alike bio-noid, the door to the interdimensional rift throws wide open, and Clancy appears, telling Ryu, Irene, and Foster that they were all used as pawns in his plan to take over the ruins and claim all the life energy as his. Foster tries to follow Clancy through the door, but the energy tears him apart and is destroyed. Ryu instructs Irene to stay behind while he goes through the rift into the subspace, as he knows that he will be protected from the power that is inside. Ryu encounters the look-alike bio-noid again while inside the subspace, who was resurrected and transmuted into a super creature. After he defeats the look-alike, Ryu is instantly teleported into a room, where he meets Clancy once again. He tells Ryu that he has already claimed the life energy as his and explains the truth behind Castle Rock – that the ruins are a dimensional warship called the "Ancient Ship of Doom". He says that "these super-dimensional ruins are the foundation upon which a new world will be created", and that it will now be where all new life will originate from. The ship reappears in the real world, and Clancy then fires a test shot from the ship into the distance to demonstrate its power, which Irene watches in horror. He then drops Ryu through a trap door to the outside of the ship.

Ryu fights back to the inner chambers of the Ancient Ship of Doom, where he prepares to engage in the final showdown against Clancy, who has now transmuted into a super bio-noid. Clancy offers Ryu to have him and Irene work for him by his side wipe out the human race and usher a new age, but Ryu refuses and commences with the final battle. After transforming twice into progressively-stronger versions of himself, Clancy is defeated by Ryu, and Ryu is transported outside the warship and back to Irene; they both watch as the Ancient Ship of Doom is brought down and explodes, and they witness the crumbling of Castle Rock fortress. In the aftermath, Ryu tells Irene that Clancy's and Foster's plan have been foiled, and that mankind will live on and refuse to be part of anyone's evil plans; he adds that mankind would never stoop to a level in which they would completely destroy themselves out of mere ambition. The two watch as the sun rises and as a new day begins.