Legions of alien Cybernetic Clones (CyClones) have devastated the Earth. Humanity's only hope lies with Havoc, himself a cybernetic warrior that had been manipulated by the CyClones to do their evil bidding. Havoc must fight the CyClones without mercy, protecting the Earth and avenging his own past.

CyClones is a first-person shooter (FPS) in which the player controls Havoc, exploring maze-like environments and blasting hostile aliens with a variety of firearms. The game is notable for pioneering the use of mouse control in games of its genre, allowing the player to aim independently of movement and move the aiming cursor to any part of the screen. Power-ups can be collected and stored in the player's inventory, bestowing combat-related benefits upon Havoc when used. Three-dimensional level maps can be brought up by pressing a key.

Another feature the game introduces to the genre is stealth. While the vast majority of the game consists of combat, there are a few stages which require the player to avoid it and stay unnoticed by the enemies, moving silently. A tutorial level also makes its first FPS appearance in CyClones, instructing the player in basic gameplay mechanics.