In Ninja Gaiden Black, Ayane's kunai messages featured fully voiced dialogue, which was not a feature in the original version. In Ninja Gaiden Sigma, the text and dialogue that explained the controls were changed to reference both PlayStation 3 controls and altered mechanics.

In the original game and the Black version, if you walk run and jump through an alleyway near the entrance to Han's Bar, you can reach a hidden shrine featuring a large metallic X, and the Windmill Shuriken embedded in an accented X-shape carved on a nearby wall. If you interact with the X, it will fully refill Ryu's Health and Ninpo. This X is the first prototype design of the Xbox console shown off at Microsoft's keynote at the Game Developers Conference 2000, and the carved design holding the Windmill Shuriken is a stylized version of the final design for the Xbox. The prototype Xbox originally appeared as a collectible item in the game's E3 2003 demo. In the Sigma version, this X is replaced with a large black monolith with Team Ninja's logo on it, while the Xbox holding the Windmill Shuriken remains intact. The healing prototype Xbox would later reappear in Ninja Gaiden II.