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Joe Musashi is a master ninja sent on a mission to release the hostages. There is one hostage per level guarded by a large guard which can either be killed or circumvented.
This is a standard 2D action platformer, however, there are mini-games between the 5 missions and 19 rounds which have the camera looking from Joe's eyes in the first person. These mini-games have the player shooting ninja stars at anything from targets to flying ninjas who have some ninja stars of their own. While playing through the main levels Joe is able to pick up different power-ups which include ninja magic, health or extra lives. The ninja magic can be used to add different abilities to the protagonist such as ninja stars or flame strikes. A health bar is present at the top of the screen and will grow with power-ups. Each level is designed with increasing difficulty and while there may be no save option in the original title once a hostage is rescued they stay rescued. The player will only have to power through the regular enemies while making their way back to the point of death. All power-ups used while killing the large guard will not respawn.
The Two-Mega cartridge used for Shinobi was unable to handle the full animations from the arcade version, but most of the sprites were kept the same. The color count in each system was slightly different, the NES version being the lowest and the Arcade being the highest.
Different versions were again limited by their cartridge capacity and console. The SMS version used BGM_A music, boss music and bonus round music. The arcade was the only edition to use digital voice, all others used analog sound effects instead.