The NES trilogy consists of the following games:
- Ninja Gaiden (NES) is the first game of the series. It follows Ryu Hayabusa on his journey through America. Having received a letter from his father to go to America and find Dr. Walter Smith should he not return, Ryu honors his father's wishes and heads there. Once in America, he encounters the Jaquio who wishes to release The Demon inside a statue. Ryu defeats the Demon after a long battle.
- Ninja Gaiden II: The Dark Sword of Chaos is the second in the series. One year after the first game, Ryu finds that his girlfriend, Irene Lew, has been kidnapped by the dark wizard Ashtar. Ryu pursues him to find that Ashtar has stabbed Irene and that Ashtar's sword feeds on chaos. After they clash, Ryu defeats Ashtar but he sends his sword along with Irene into the realm of chaos. Ryu follows and encounters Jaquio who was thought to have been killed, after defeating him, the dark sword resurrects Jaquio as a giant monster. Ryu summons all his strength and defeats the beast.
- Ninja Gaiden III: The Ancient Ship of Doom is the third and final game in the NES trilogy. It is set between the events of the first two games. Ryu, having been framed for the murder of Irene, must clear his name. Ryu encounters Foster, the director of the CIA who unleashes his suped up doppelganger on Ryu. Ryu is bested but spared. Not letting this set back get to him, Ryu wanders on and makes it to Foster's castle where Foster reveals his plans but is interrupted by the arrival of Irene, who faked her death to institute a raid on Foster. Ryu faces the doppelganger again and wins. With everything else out of the way, Clancy, Ryu's ally reveals himself to be the real villain and Ryu must face a robotized version of Clancy. He does so and manages to win.