Set in the year 2029, the evil dictator Emperor Garuda has taken over the United States of America, building a stronghold in the middle of the nation's "largest city". To stop Garuda and avenge the innocent lives that were lost in his reign, two ninja from the Iga clan, Hayate and Kaede, are hired to infiltrate Garuda's stronghold and assassinate him.
Shadow of the Ninja can be played by up to two players simultaneously, with one player controlling Hayate (the male ninja) and the other as Kaede (the female ninja). In either mode, the player can decide which character they want to control before the game actually begins. There are no actual performance differences between either character.
Source: Wikipedia, Shadow of the Ninja , available under the CC-BY-SA License.