Shinobi , the final installment of the series on the Nintendo 3DS, follows the story of Joe Musashi as he returns to Japan to recover from his battle with the Neo Zeed organization. However, upon his return, he senses that the Neo Zeed leaders are secretly rebuilding the organization, prompting him to make another attempt to defeat them.
The gameplay is very similar to its predecessor, a side-scrolling action-adventure game with platform elements. Musashi uses kunai and a sword as weapons, which can be upgraded by collecting power-ups inside crates. The game introduces new movements to Musashi's repertoire, including the ability to block enemy projectiles, drop-kick enemies, dash, slash, and perform wall jumps. Four ninjitsu are also available, providing temporary invincibility, whole screen fire attacks, higher jumps, and self-destruction.
The game is divided into seven rounds, each with two parts and a boss at the end of each part, except for the last round which features only one final boss. Most levels feature horizontal scrolling from left to right, while some also include vertical scrolling. The game rewards different playing styles, granting extra points for completing levels without using certain items and awarding additional lives based on point scores.