The Revenge of Shinobi takes place three years after the first game, the criminal organization Zeed from the original game has since reformed and have renamed themselves “Neo Zeed”. They decide to have their revenge on the Oboro Ninja clan and Joe Musashi by killing his master and kidnapping Joe’s bride, Naoko. Joe, having reached the clan too late, manages to learn about Neo Zeed’s plot by his dying master. Joe decides to travel the world to gain his revenge on Neo Zeed as well as try to save his bride before it’s too late.
Because of copyright issues regarding certain enemy characters (many of which were based on cultural icons) there were at least four versions of the game in Japan and North America, with the later two also appearing in Europe.
- Software revision 1.00 (1989): Enemy characters resembling Rambo, The Terminator, Spider-Man, Batman, and Godzilla are present. Both Spider-Man and Batman are actually fake representations of the characters conducted by a shapeshifter who alters his appearance after sustaining a certain amount of damage. Additionally, Joe Musashi’s face on the title sequence resembled that of actor Sonny Chiba dressed as his character Hattori Hanzō from the Japanese TV series Shadow Warriors (Kage no Gundan).
- Software revision 1.01 (1989): Batman is replaced by a winged Devilman-like creature. Godzilla and Spider-Man remain unmodified, the latter now morphs into the Devil when defeated. The “Gunner” enemy soldiers with flamethrowers are also changed to bald men with headbands, altering their original likeness to Rambo (although Sega had the license to the character for their Rambo III console games, they did not use it for this game).
- Software revision 1.02 (1990): The fake Spider-Man is now redesigned into the licensed character from Marvel Comics, acknowledged by a copyright notice (Sega already had the license to the character for their game The Amazing Spider-Man vs. The Kingpin). Since he is now the real Spider-Man, he does not morph into the Devil and actually leaves the battle when enough damage is inflicted, with the winged Devil entering to replace him. Godzilla still remains intact.
- Software revision 1.03 (1990): Godzilla is replaced by a skeletal dinosaur. Everything else remains intact from the previous revision, including the licensed use of Spider-Man. This version was used in the Genesis 6-Pak cartridge along with the “Sega Classics” edition of the game.
- Software revision 1.04 (2009/2012): Since the licensed use of the boss Spider-Man was for a limited period of time, the game was subsequently prevented from being re-released years later. The 2009 release for the Virtual Console as well as the Xbox Live Arcade and PlayStation Network 2012 releases features a new specific software revision (1.04) that omits the Marvel copyright notice and replaces Spider-Man with a pink palette swap of the character that still behaves the same as the licensed Spider-Man. Joe Musashi’s design in the title screen was also altered to remove his likeness to Sonny Chiba.
The credit roll, shown when achieving a “good” ending, was removed from the non-Japanese versions of the game. In versions 1.00 and 1.01, “©SEGA 1989 / MUSIC ©1989 YUZO KOSHIRO” would be shown at the bottom of the title screen like normal; when the Spider-Man copyright notice was added to the game, all copyright bylines were moved to a screen displayed before the intro.
The game is a traditional side-scrolling platform game. The player controls Joe Musashi and must complete eight districts before the final confrontation with the head of Neo Zeed. Each district consists of three scenes, two of which are platforming levels and the third being a battle against a unique boss-character.
The directional pad moves Joe around while the A, B, and C buttons are used to perform ninjitsu techniques, attack, and jump respectively. A key move in The Revenge of Shinobi is the somersault, which maximizes Joe’s jumping height and enables him to throw eight 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.
Although his standard ability of moves and attacks, Joe has the ability to do four special ninjutsu techniques. Only one can be performed in each level, unless a ninjitsu item was picked up, or the ninjutsu of Mijin was used.
A variety of bonus crates can be found in each level, some hidden in the scenery. These include simple powerups such as extra shuriken or health packs, as well as special items to gain lives or extra ninjutsu attacks. Besides powerups, some crates may contain time bombs: explosives that detonate when their fuse runs out or if Joe 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. As difficulty increases, more enemies appear per stage; on Hardest, Musashi takes twice as much damage 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 technique does exist that allows infinite shuriken).