Naious is a horizontally scrolling shoot-em-up. The gameplay is fairly traditional and involves navigating outdoor and indoor stages (often with narrow spaces), destroying mobile and stationary enemies on the way. The fighter craft starts with a vulcan gun and can later change to wide shot, laser, and homing missiles. Rather infrequent power-ups appear at set points on the stages and change or enhance the plane's weapons.

In 21th century the Earth became overpopulated, and humans began building colonies in the solar system. Technological expansion led to widespread pollution; in order to counter it, a powerful computer Naious was built. One century later, humans became completely dependent on Naious, and that was when it stroke unexpectedly. European cities were reduced to ruins after a single attack. The fighter spacecraft ASP and its pilot Manami Katagiri were dealing with a possible rebellion on Jupiter when it became clear that the future fate of humanity depends on them.