The game is a sequel to Shinobi, a 1987 arcade game, and boasts an acclaimed soundtrack by the famous video game music composer Yūzō Koshiro. The game was included in the compilations: Mega Games 2, Mega Drive 6 Pak, Sega Classics Arcade Collection (for Sega CD), and Sega Smash Pack (for the PC and Dreamcast). It was re-released for the Wii Virtual Console in 2009.
The introductory game screen features famous martial arts actor Sonny Chiba dressed as Hattori Hanzō from the popular Kage No Gundan TV series.
Taking place three years after the first game, the criminal organization Zeed from the original game has since reformed and have renamed themselves "Neo Zeed" (literally "New Zeed"). Neo Zeed decide to have their revenge on the Oboro Ninja clan and Joe Musashi by killing his master and kidnapping Joe's fiance, Naoko. Joe, having reached the clan too late, manages to learn about Neo Zeed's plot by his dying master. Joe sets out on a journey around the world to gain his revenge on Neo Zeed as well as rescue his fiance before it's too late.
The game is a traditional side-scrolling platform game. The player controls Joe Musashi and must complete 8 districts before the final confrontation with the head of Neo Zeed. Each district consists of 3 scenes, the last of which is a battle against a unique boss-character.
The D-pad moves Musashi around while the A, B and C buttons are used to perform a ninjitsu technique, attack and jump respectively. A key move in The Revenge of Shinobi is the somersault, performed by pressing the jump button and then pressing it again at the height of a jump. The somersault maximizes Musashi's jumping height and enables him to throw 8 shuriken at once in mid-air. Additionally, some stages consist of multiple layers, such as the first scene of the Military Base and the freeway in Area Code 818. Switching between layer (outdoor/indoor, or on-the-highway/next-to-it) is also done with the somersault move.
Besides his regular assortment of moves and attacks, Musashi has the ability to perform four special ninjutsu techniques. Only one can be used in each level, unless an additional bonus was picked up or the ninjutsu of Mijin was used to reset your life total. The four ninpo techniques employed by Joe Musashi are as follows:
- Ninjutsu of Ikazuchi (the art of thunder): Envelopes Musashi with a shield of lightning energy that sustains damage for four consecutive hits.
- Ninjutsu of Karyu (the art of fire): Summons four dragon-shaped columns of flame that move across the screen and damage all enemies in their path.
- Ninjutsu of Fushin (the art of floating): Improves Musashi's agility by heightening his jumping capability.
- Ninjutsu of Mijin (the art of pulverizing): The most powerful ninjutsu technique in the game. Musashi explodes, damaging all enemies on screen at the cost of one life (Note that it is actually possible to use this Ninjitsu on your last life; however, it is most unwise, as if the player does not have a life to spare after its use, Mijin causes the game to end a stage in Musashi's death, causing a continue to be used in order to carry on with the game). This ninjitsu is a very interesting and strategic Ninjitsu to use, as when Musashi uses Minjin, his health is fully restored, and he is also granted an EXTRA ninjitsu attack when he recovers. Minjin will, like Karyu, destroy all normal enemies on screen, however with this Ninjitsu, Musashi's power against boss enemies is much greater.
A variety of bonus crates can be found in each level, some hidden in the scenery. These include simple power-ups such as extra shuriken or health packs, as well as special items to gain lives or extra ninjutsu turns. Besides power-ups, some crates may contain time bombs: explosives that detonate when their fuse runs out or if Musashi comes too close (though he can walk out of the blast radius if the player is quick enough).
The game is divided into four difficulties: Easy, Normal, Hard, and Hardest. As difficulty increases, more enemies appear per stage, Musashi takes twice as much damage on Hardest and the amount of starting lives decreases from 10 to 1. From the options menu, the player can also choose the amount of starting shuriken from 0 to 90 (though a code does exist that allows infinite shuriken).
- Ibaraki Province, Japan: This bamboo forest is where the game begins. Through these ancient ruins Musashi must make his way to The House of Confusion. At the end of this district, he is confronted by the mighty samurai Blue Lobster.
- Tokyo: Musashi begins this stage near a rocky canyon. Winged ninja swoop down from the sky to attack Joe. Once he makes it past the waterfalls, the district moves on to the darkened roof tops of Tokyo, and eventually into a blinding disco where Joe confronts the Shadow Dancer.
- The Military Base: The military complex of Neo Zeed is heavily guarded by armed soldiers, flamethrowers, and attack dogs. Musashi will encounter liattack dogs. The second scene takes Musashi on board an air carrier. If he touches one of the air locks, he dies. The aircraft is controlled by a powerful supercomputer that houses a human brain.
- Detroit: Detroit is one big Wreck yard|junkyard, heaps upon heaps of cars, running through conveyor belts and into a melting furnace. A tough muscleman android guards this wreckage.
- Area code 818: This stage takes Musashi past skyscrapers and freeways. The final battle is fought on top of an armoured vehicle carrying a gigantic ballistic missile.
- Chinatown: After a showdown with the kung-fu gangs of Chinatown, Musashi hops on board a speeding train. Eventually, he finds himself in the clutches of a pink humanoid/bat-like hybrid creature known as Web-Bat.
- New York: Ninja and machine gunners guard the breakwater of New York's dockside. Leaping from boat to boat, Joe infiltrates Neo Zeed's container ship and comes face to face with a fire-breathing skeletal dinosaur.
- Neo Zeed Marine Stronghold: Here is where Musashi faces his final enemy, who appears to be the leader of Zeed himself. The beautiful Naoko is trapped somewhere beneath the cellar maze of this stronghold, and Joe must quickly terminate the boss of Neo Zeed, known as the Ninja Master, before the cell trap kills Naoko.