In a future where fossil fuels are limited, major countries and forces of the world are at war with one another over territory. Alliances are made, forming two major sides: The Axis and The Federation. The elite units in these wars are Assault Suits, man-piloted combat mechs called Assault Suits. Jake is one such pilot, drafted into the Pacific States' Marine Corp under the Federation. During his training, the war has grown substantially and upon being assigned to a platoon, he is immediately thrown into combat.

Cybernator is a side scrolling mech combat game and platform game. The player controls Jake as he moves his assault suit left and right on the battlefield. The assault suit can jump and use a jetpack for a short time to increase altitude. The assault suit begins with a Shot machine gun weapon that spreads out fire in front, and a Punch weapon for close melee. Additional weapons can be found during the course of the game and existing weapons improved by the gathering of "P" power-ups left by defeated enemies.

Each level contains a variety of enemies and an end boss which must be destroyed to reach the next level. Some levels take place as horizontally scrolling shooters, in which the Assault suit can move up, down, left and right on the screen, but is constantly advancing towards new threats.

The PlayStation 2 version is not a straight port or emulation of the original SNES game. It has altered visuals and balance tweaks, as well as a brief new stage at the beginning.