The objective of Warheads for Windows is to keep your cities alive. You do this by firing Anti-Ballistic Missiles at incoming enemy missiles. If any enemy missiles are in the neighborhood when your ABM explodes, they are destroyed. If an incoming missile reaches one of your Cities, it will cause a Humongo Nuclear Explosion and kill everyone in the city (this is not good!!!).
This Missile Command variant puts the player in control of two missile bases, each controlled by a different mouse button. As warheads, planes and smart bombs attack the player's cities, he or she must fire missiles at them by pointing the mouse at a target area and clicking the appropriate button. Ammunition is limited and missile bases can be completely destroyed by enemy fire, so a mix of strategy and coordination is necessary for success.