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". 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.
- Ibaraki Province, Japan
- This bamboo forest in the Ibaraki Prefecture is where the game begins. Through these ancient ruins Joe must make his way to The House of Confusion. At the end of this district, he is confronted by the mighty samurai Blue Lobster.
- Joe begins this stage near a rocky canyon, assaulted by winged ninja. 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 must battle with the Shadow Dancer.
- The Military Base U.S.
- This military complex of Neo Zeed is heavily guarded by armed soldiers. Joe will encounter light infantry as well as flame throwers and attack dogs. The second scene takes Joe 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 is one big junkyard, heaps upon heaps of cars, running through conveyor belts and into a melting furnace. A tough Terminator-like android guards this wreckage.
- Area Code 818
- Area code 818 takes Joe past skyscrapers and freeways. The final battle is fought on top of an armoured vehicle carrying a gigantic ballistic missile.
- After a showdown with the kung-fu gangs of Chinatown, Joe hops on board a speeding train. Eventually he finds himself in the clutches of characters resembling Spider-Man and Batman (Devilman for the 1.01 version of the game). In the PAL Mega Drive manual, the boss is described as a single shapeshifting character known as the Web-Bat.
- New York
- Ninja and machine gunners guard the breakwater of New York City's dockside. Leaping from boat to boat, Joe infiltrates Neo Zeed's container ship and comes face to face with Godzilla (turned into a dinosaur skeleton in version 1.03, referred to as a brontosaurus in the PAL manual).
- Neo Zeed Marine Stronghold
- Here is where Joe faces his final enemy, the leader of Neo Zeed. After passing by the Marine, Joe needs to find the right way on a large and well-guarded labyrinth. The beautiful Naoko is trapped somewhere beneath the cellar maze of this stronghold, and Joe must terminate the Boss quickly before the cell trap kills Naoko. There are two endings to the game, depending on whether Joe defeats the Boss in time to save Naoko.
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. The four techniques employed by Joe are as follows:
- Jitsu of Ikazuchi: Surrounds Joe with a protective shield of lightning energy that sustains damage for four consecutive hits.
- Jitsu of Karyu: Produces four dragon-shaped columns of flames that move across the screen and damage all enemies in their way.
- Jitsu of Fushin: Improves Joe's jumping ability.
- Jitsu of Mijin: Joe explodes, damaging all enemies on screen at the cost of one life. The suicide has the side-effect of restoring health and ninjutsu.
The Revenge of Shinobi is conisdered the best in the Shinobi series. The game received 8/10 from IGN, and 5/5 in Dragon; the final boss battle was criticised, however, for being too difficult. MegaTech magazine praised the "smart gameplay, graphics and sound". Mega placed the game at #18 in their Top Mega Drive Games of All Time. Reviewing the game's appearance in Sega Arcade Classics, Glenn Rubenstein said it "was one of the first Genesis games released, and it shows how far Sega has come since then."
The Revenge of Shinobi introduced many new moves for Joe Musashi, and its famed soundtrack composed by Yuzo Koshiro is considered the best on the Genesis. A suite of music from the game was performed live by an orchestra at the Fourth Symphonic Game Music Concert in 2006 at the Gewandhaus zu Leipzig, Germany. The arrangement was done by original composer Yuzo Koshiro himself. Music from The Revenge of Shinobi was also performed at two concerts of PLAY! A Video Game Symphony in Stockholm, Sweden in 2007. It was also played during the encore as the most voted song when PLAY! A Video Game Symphony was performing in Singapore (June 2007).