Mystery Island II takes elements from puzzle games, adventure games, and science fiction to create a fun and interesting experience.

You are a Navy Seal currently serving aboard the USS Volarus when your submarine is destroyed by an unidentified vessel. A Russian nuclear warship seems the most likely possibility. You escape the final blast and wash up on a tropical island. The situation, as you find out, is a much more grim that you originally anticipated. The fate of humankind now rests in your hands.

Players must find and use items to progress further in the game, ensure they stay alive, and finally defeat the aliens, saving Earth.