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Shinobi is a linear game. You must clear 5 missions, with each mission consisting of 3 or 4 stages. Only the first mission has 3 stages, while the remaining missions have 4 (for a total of 19 stages). In every stage except for the final stage of each mission, you must find a rescue all of the children being held hostage. You cannot proceed to the next stage until you rescue all of them.

Among the children hostages, there is one who possesses a power-up function. Upon rescuing this child, your shuriken attacks will switch to a gun attack, and punch and kick attacks will switch to a ninja sword attack.

In the final stage of each mission, a boss enemy will appear. You can only proceed to the next mission by defeating the boss character.

There is a bonus stage between each mission. These bonus stages have a 3D perspective. You can earn bonus points by defeating all the enemy ninjas that are running towards you from the back of the screen. If you miss even one enemy, a ninja will appear in front of you on the screen and you will not be able to earn bonus points.