Warheads for Windows is a clone of Atari's popular 1980 arcade game, Missile Command. Originally it was pretty much a straight rip-off of the classic "intercept the falling missles" game, where you had two missile launchers (instead of three) that you could use to shoot down incoming missiles (the left and right mouse buttons fire from the left and right missile launchers, respectively) to prevent them from destroying six cities below. The missile launchers have a finite number of missiles and can be destroyed by missiles. You earn points for shooting down missiles, nukes and airplanes, and for each city that survives each round, which can earn bonus cities which replace destroyed cities.

When you have no cities left, the game is over. Version 2.0 added sound card support; a large number of configurable options; a display of how many missiles each launcher has remaining; branching missiles (MIRVs), and "blossoming" explosions, in which the destroyed missiles blow up and can destroy the other missiles, causing a chain reaction of destructions. Most of the configurable options are only available in the registered version.