A force of alien invaders has descended upon the Earth and has wiped out humanity for the most part. Some ninjas survived the onslaught, however, and two ninjas in particular, named Blade and Talon, are assigned to rid the planet of this alien menace.

Ninja Crusaders is a side-scrolling action game that can be played alone or with two players fighting side by side. A ninja player can jump quite high and begins the game with a ninja throwing star weapon that can travel the length of the screen, although it's not very powerful. Other weapons are available for the taking throughout the levels, each with considerably less range than the stars but with more power. These weapons include a chain whip, a sword, and a bo staff.