Shinobi is the sequel to The Revenge of Shinobi and the last installment of the series on the Nintendo 3DS. After defeating the Neo Zeed organization, ninja Joe Musashi returns to Japan to recover from the battle. But while he's training, he senses that the Neo Zeed leaders are secretly rebuilding the organization, so he makes his way back to defeat them once again.
The gameplay is very similar to the previous game, a side-scrolling game with platform elements. Musashi uses kunai (throwing knives) and a sword as weapons and can upgrade their power by picking up power-ups inside crates. Inside those crates he will also find extra lives, health, kunai (5 or 20), ninjitsu, and time bombs that will explode in 5 seconds or immediately if touched.
The gameplay is divided into seven rounds, each subdivided into two parts with a boss at the end of each part. Most levels feature horizontal scrolling from left to right, but some levels will also feature vertical scrolling. There are three forced scrolling levels: two horizontal and one vertical. The game features four difficulty levels, including normal difficulty, where the player has 3 lives and 3 continues.