The Nakatomi company is searching for the pieces of the Akujiki sword, shattered by Hotsuma in the predecessor, Shinobi. Luckily, the Oboro ninja clan has since reformed. As Hibana, kunoichi (female ninja) of the Oboro clan, you are charged with the task of finding the pieces of the Akujiki before Nakatomi does.

Nightshade is a sequel to Overworks' Shinobi for the PS2. Like its predecessor, it features several levels full of challenging enemies to fight using a combination of your sword, shuriken, and magic scrolls. Speed and stealth remain the emphasis, as you use stealth dashes and the ability to walk on walls to perform long strings of kills called tates. One of the main improvements to the gameplay system is the ability to create much larger combos/tates. In order to facilitate this, they've expanded the battle system to include flying kicks to break your opponent's guard and stealth attacks to kill unsuspecting foes in a single blow.