Musashi's ninjutsu techniques can only be used once per stage and will clear the screen of all enemies, or in the case of enemy bosses, greatly damage them. When powered up, his throwing stars are replaced by a gun that fires large, explosive bullets, and his close-range attack becomes a katana slash. Rescuing certain hostages in each stage will grant him an attack upgrade. Musashi's standard weapons are an unlimited supply of shurikens, along with punches and kicks when attacking at close range. The player can jump to higher or lower floors by pressing the jump button while holding the joystick up or down. In addition to the standard walk, the player can perform a crouching walk by pressing the joystick diagonally downward. The controls of Shinobi consist of an eight way joystick and three action buttons for attacking, jumping and using ninjutsu techniques (also called 'ninja magic' in the game). At the start of each mission, the player is shown their objective, followed by a file containing a photograph of the enemy boss and a map display pinpointing the location of the next stage. Through five missions (consisting of three stages for the first mission and four stages each for the rest), Musashi must make his way to Zeed's headquarters and free all the hostages in the first two or three stages before confronting the boss at the final stage of each mission.

The player controls a ninja named Joe Musashi who has to stop a criminal organization called 'Zeed' who are kidnapping the children of his ninja clan. In Shinobi, the player controls a modern day ninja named Joe Musashi who goes on a mission to rescue his kidnapped students from a group of terrorists. Shinobi (Japanese: 忍 -SHINOBI-) is a side-scrolling action game produced by Sega originally released for the arcades in 1987.

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