Cybernator takes place in a future where nations are fighting over territory due to limited fossil fuels. The war has led to two major alliances: The Axis and The Federation. Jake is an elite pilot in The Federation, piloting an Assault Suit called Cybernator . He's drafted into the Pacific States' Marine Corp during his training and thrown into combat immediately.
The gameplay involves controlling Jake's Cybernator as he moves left and right on the battlefield. The mech can jump and use a jetpack for short periods, increasing its altitude. Initially, it comes equipped with a machine gun that fires in front of it and a punch weapon for close combat. Players can find additional weapons and improve their existing ones by collecting "P" power-ups from defeated enemies.
Each level features various enemies and an end boss that must be destroyed to progress. Some levels are horizontally scrolling shooters, where the Cybernator can move up, down, left, or right while advancing towards new threats.
The PlayStation 2 version of Cybernator is not a direct port of the original SNES game. Instead, it has altered visuals and balance tweaks, as well as an additional stage at the beginning.