CyClones is set in the closing of the 20th century, when wars and pollution devastated many countries in the world and led to a policy of isolation for many governments.

A remarkable discovery about the alien invasion was that most of the invaders were cloned from human tissue samples, genetically engineered, and then cybernetically enhanced.

The player controls the "HAVOC unit" in a series of missions given by the Earth government to confront and push back the alien invaders and their clone servants.

The gameplay follows the standard first-person shooter formula set by Doom the year before, requiring the player to navigate several levels while fighting enemies and activating switches or seeking keys to gain access to different areas.

The player can find medikits and "mech-kits" (which serve as armor) in order to ensure their survivability, as well as acquire several weapons which are either human or alien in origin.

Development for CyClones started in early 1994, when Raven Software's developers split in two teams: one working with id software's Doom engine to create a fantasy game which later evolved into Heretic, while the other team started on a project that was to use the engine from ShadowCaster to create a futuristic first-person shooter game for Strategic Simulations.