12 missions that take place during the night, dusk and day, for both Rikimaru and Ayame, plus a two-level training mode. New mission objectives include stopping an enemy invasion, protecting a princess, guarding the Palace, stealing objects, assassination and tracking enemies. Players can create their own missions and maps, place objects and enemies, determine AI behavior and then save their creations to a Memory card to exchange with friends. Ninja short and long-range weapons and items. Players have the ability to use a multitude of authentic weapons including swords, knives, a blow gun, bows with exploding arrows, blinding dust, throwing stars, grenades, and the magic vanishing tree.
Players can now search defeated enemies and take weapons in their possession.
Players will be able to execute new and varied stealth kill techniques with 6-7 moves per character.