The Ninja Warriors presents side-scrolling hand-to-hand combat. Players take control of Kunoichi or Ninja and fight wave after wave of Banglar forces across five levels.

The game is based in a dystopian future where Banglar, the President of the United States in 1993, issues martial law on the nation, with the military having total control over the law. A group of anarchist scientists led by Mulk decide that it is time to revolt against the government. Knowing full well that approaching the military themselves could be considered an all out suicide mission, the scientists create two androids that can sustain various forms of damage in order to do the mission for them. The robots, code named "Kunoichi" (red female) and "Ninja" (blue male), are sent by the scientists in order to end Banglar's tyranny once and for all.

Ninja and Kunoichi each have different combos — one to be executed normally, and another that can be performed while crouching — and specific moves such as dash attacks, throwing, stabbing and air strikes. On the screen, separate from the life bar, there is a special energy bar that fills itself as the main character progress. When full, the bar will allow the player to perform a special move. If the character suffers some damage, the special bar will reset, starting a new count-up.