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. 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. 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.

• Mission 1: "Pursue the Terrorists" - Set in the slums of a city. The boss is Ken Oh, a gigantic samurai-like ninja who can throw fireballs.
• Mission 2: "Enter the Enemy's Hide Out" - Set in a harbor. The boss is the Black Turtle attack chopper, which drops off an army of yellow-clad ninjas.
• Mission 3: "Attack the Logistic Base" - Set in a secret base hidden within a cave. The boss is a lineup of stack-up Mandara statues controlled by a supercomputer, which takes the form of a giant fireball-spitting face.
• Mission 4: "Destroy the Enemy Ninja Group" - Set in a ninja training camp. The boss is the Lobster, a tall sword-wielding ninja clad in red samurai armor with a V-shaped symbol on his helmet.
• Mission 5: "Defeat the Behind-the-Scene Ninja" - Set in the mansion of the enemy's leader. Unlike previous missions, the player is not allowed to continue if he loses all of his lives at this point. The final boss is Zeed's leader the Masked Ninja, who attacks with four different ninjutsu techniques. His true identity is revealed to be Nakahara, Joe Musashi's mentor. Nakahara's name is a reference to the Musashi-Nakahara Station. His name is meant to be a hint of his true identity as "Nakahara Musashi", Joe Musashi's father.

The game was well received by Clare Edgeley of Computer and Video Games, although she repeatedly called the game Shenobi.

Master System

Sega produced its own home version of Shinobi for their Master System game console. It was released in Japan on June 19, 1988, with subsequent releases in North America and Europe. Some of the play mechanics from the original coin-op version were altered for this version. Instead of the one-hit kills from the arcade game, the player now has a health gauge that allows Musashi to sustain more damage before losing a life, although this comes with the trade-off that touching an enemy causes Musashi to lose health.

While the player still rescue hostages in this version, it is now an optional task and not mandatory to complete the game. However, rescuing hostages allows the player to upgrade both, their close and long-range weapons, as well increase their maximum health gauge or restore it. Additionally, rescuing certain hostages is a requirement to access the game's bonus stages, which now occur after the regular stages instead of each boss fight. The ninjutsu skills are now obtained from completing these bonus rounds and the player may hold up to four stocks. The input method of performing these ninja arts is also different as well. The player can use between three different close-range weapons (in addition to the default punches and kicks), four long-range weapons (including an upgrade to the default shurikens), and six ninjutsu spells.

Home computers

In 1989, ports of Shinobi were released for the Commodore Amiga, Atari ST, Commodore 64, Amstrad CPC, and ZX Spectrum. All five conversions were developed by The Sales Curve and published by Virgin Mastertronic in Europe and by Sega in North America (with the exception of the Amstrad and Spectrum versions). An IBM PC version was also released in North America by Sega, developed by Micromosaics Inc.

PC Engine

A PC Engine version was released exclusively in Japan by Asmik on December 8, 1989. The graphics and play mechanics of the PC Engine version are similar to the arcade version's, but the close-range attacks and power-ups are missing and there are no bonus rounds (extra lives are instead given by getting a certain amount of points). Although, there is no life gauge, the time limit for finishing each stage from the arcade version was removed. Mission 2 is also completely omitted and all subsequent missions are renumbered as a result.

Nintendo Entertainment System

The Nintendo Entertainment System version of Shinobi was released by Tengen exclusively in North America as an unlicensed release in 1989. The play mechanics are based on the Master System's version. However, Tengen removed all of the close-range weapons (the sword, the nunchaku, and the chain) and the grenades. Only the basic punches, kicks, throwing daggers, and pistol were kept. Unlike the Master System version, the player can only shoot one shuriken, dagger, or bullet on-screen at the same time, even after obtaining power-ups. However, the maximum stock of ninjutsu skills has been increased to five. All the vertical-scrolling stages (such as Mission 2-2 and Mission 3-2) were redesigned into horizontal-scrolling stages.

Wii and Xbox 360

The original coin-op version is available as a downloadable title for the Wii's Virtual Console and Xbox 360's Live Arcade services. Although both releases are emulated from the arcade game's code, slight graphical modifications were made due to licensing issues.

One of the enemy grunts in the second stage of Mission 1, a wall-crawling ninja who roughly resembles the comic book character Spider-Man, originally wore a blue bodysuit and mask with red gloves and boots, which was too close to Spider-Man's color scheme. In the Wii and Xbox 360 releases, his color scheme was changed to a green bodysuit and mask with yellow boots and gloves.

The backgrounds in Mission 1-2 and 1-3 also featured Andy Warhol-style posters of Marilyn Monroe. However, without consent from the Monroe estate, these images had to be removed.

Sonic's Ultimate Genesis Collection

Shinobi is also a hidden game in Sonic's Ultimate Genesis Collection for the PlayStation 3 and Xbox 360. To access it, the player must complete the first round of Shinobi III: Return of the Ninja Master, without using a continue. Although the version included in the compilation was also an emulation of the arcade game, the graphical changes that were made in the Virtual Console and Xbox Live Arcade releases were not made in this compilation.

In 1989, Sega released a follow-up called The Revenge of Shinobi as one of the first titles for their new Sega Mega Drive game console. In Japan this game was called The Super Shinobi.

An arcade sequel called Shadow Dancer was also released in 1989. Shadow Dancer retains the same gameplay as the original, but gives the main character a canine companion.

Other Shinobi sequels also appeared for the Game Gear, Mega Drive/Genesis, Sega Saturn, and, most recently, the PlayStation 2 in a new storyline involving a new character named Hotsuma.

Alex Kidd in Shinobi World is a parody of Shinobi with former Sega mascot Alex Kidd as the main character, released for the Sega Master System in 1990.