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. 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.