- The arcade game ending. After you beat the final boss, Ryu is suddenly napping in a boat being driven by Muramasa, heading towards Japan. The skyline contains every one of Japan's most well-known landmarks, including Mt. Fuji and Tokyo Tower, which are miles upon miles apart in real life.
- The infamous Japanese Commercial for Ninja Gaiden Sigma 2 that made the Jiggle Physics controllability feature famous.
- In the Xbox game, Ryu's outraged expression upon interacting with a badly repaired window in Chapter 3.
Ryu: What a careless repair job! Are they trying to make fun of Ninjas?