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 apparent 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 to the Castle Rock fortress, where he will give Ryu more information about Irene when he gets there.
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 apparent 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 to the Castle Rock fortress, where he will give Ryu more information about Irene when he gets there.