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 decides to travel the world to gain his revenge on Neo Zeed as well as try to save his fiance before it's too late.
FROM THE BACK OF THE BOX:
You are Musashi, master ninja. You are one of the mystic warriors, who see and know all things. You are deadly! Now you must destory the vicious army of Neo Zeed. If you fail, then Naoko, their beautiful prisoner, dies!
Attack with a ninja sword and crossed daggers! Somersault over fences while hurling deadly knives! Ward off bullets, Death Stars, and junked cars by leaping, twisting, and kicking!
The Neo Zeed are masters of disguise! But you are a master of Shinobi, the art of Stealth. You'll stalk the Neo Zeed through 24 treacherous scenes, while they stalk you!
Battle ninjas, musclemen, deadly lasers, and the diabolical Boss! Outfight Kung Fu gangs and armies of machine gunners. The Neo Zeed is almost unstoppable, but you have a secret weapon - ninja magic!