Ninja Gaiden Trilogy contains the first three Ninja Gaiden games (Ninja Gaiden, Ninja Gaiden II: The Dark Sword of Chaos, and Ninja Gaiden III: The Ancient Ship of Doom). The game was released for the Super Nintendo Entertainment System in 1995, developed and published by Tecmo. There were many changes made to the games beyond graphical updates. Due to Nintendo's family friendly policy, several instances of blood or religious material (pentagrams, specifically) were removed. Ironically, some lines were altered from their previously censored version, adding words such as "damn" that were previously unseen. The difficulty in Ninja Gaiden III was altered to be slightly easier and more reasonable, and several music tracks were changed.
The first game in the series and the first in the compilation was originally released in 1988. Ryu Hayabusa is the star of Ninja Gaiden, as he searches for his missing father, Ken, in the United States. Ryu first meets a Dr. Smith, as instructed in a note from his father. Smith talks about two demon statues that have the power to summon an ancient devil and possibly end the world. One of the statues is stolen, Ryu is contacted by the CIA, and Ryu ends up traveling to South America to track the statue down, as well as the leader of an evil cult (known as Jaquio), who is intent on resurrecting the demon. In the end, Ryu manages to defeat Jaquio, and is reunited with his father.
Ninja Gaiden II
The Dark Sword of Chaos continues the plot of Ninja Gaiden. Ryu gets word of a villain named Ashtar (the Emperor of Chaos and mentor to Jaquio). Irene Lew, the CIA agent that Ryu worked with in the first game is kidnapped by Ashtar. Ryu's main goal is to track down both the weapon forged from a bone of a demon (the Dark Sword) as well as Irene Lew. After facing Ashtar and defeating him, Ashtar sends Irene, the Dark Sword, and Ryu into the Realm of Chaos with his dying breath. Here, Ryu finds a resurrected Jaquio, who he manages to defeat once and for all.
Ninja Gaiden III
The final game in the trilogy actually takes place sometime between the events of the first and second game, and involves a mystery in which Ryu is framed for the murder of Irene Lew. Ryu discovers that two CIA agents (Clancy and Foster) were involved in a paranormal experiment involving the energy created when Ryu defeated the demon in the first game. This experimentation resulted in the creation of several doppelgangers, or "bio-noids," one of which appeared to be Ryu Hayabusa. It was this one that murdered Irene Lew. After uncovering this entire plot, Ryu fights both the bio-noids, Foster, and Clancy, ending in an epic confrontation in the Ship of Doom (an incredible warship which has the sole purpose of the destruction of humanity), where Ryu destroys the ship and kills everyone involved in the bio-noid plot.