A year after the events of the original Ninja Gaiden, a new villain named Ashtar receives word of Jaquio's defeat. Ashtar uses this opportunity to hatch a new plan to plunge the world into darkness. The ninja, Ryu Hayabusa, hits the trail to destroy all manner of vile creatures entering the world while fighting his way to destroy Ashtar, his Dark Sword of Chaos, and whatever else is behind the evil.

Ninja Gaiden II: The Dark Sword of Chaos is a fast paced, side scrolling action game in the tradition of the original Ninja Gaiden game. Ryu is a ninja who can run, jump, and slash with his ninja sword. He can also attach to vertical walls and climb up and down, which is an ability missing in the previous game. Powerups are hidden everywhere throughout the levels. These powerups include fireballs and ninja stars as before; a unique new powerup is the ninja shadow. Ryu can collect up to 2 ninja shadows that follow his every movement and use the same weapons at the same time that Ryu strikes.

Ninja Gaiden II tells its story through liberal use of cinematic scenes interspersed between the action levels. Different levels feature a variety of environmental interaction; e.g., one level has Ryu on a high mountain where snow is falling fast and the wind is blowing hard. The shifting direction of the snowfall indicates how the wind is blowing and Ryu has to fight against the breeze. In a night level, much of the environment is dark and is illuminated only sporadically by flashes of lightning.