Nightshade follows Hibana, a kunoichi of the Oboro ninja clan, as she attempts to find the pieces of the Akujiki sword before Nakatomi can. The company is searching for these fragments, which were shattered by Hotsuma in the predecessor game Shinobi .
The gameplay focuses on speed and stealth, with an emphasis on using a combination of sword, shuriken, and magic scrolls to defeat enemies. The player must use stealth dashes and wall-walking abilities to perform long strings of kills called tates, with the option to create larger combos through the expanded battle system.