UFO: Aftermath is the first in a three-game squad-based tactical strategy-RPG series clearly inspired by the original X-COM games, with similar themes and gameplay, but with its own post-apocalyptic horror spin on the concept. The game is rendered in isometric 3D.

In the year 2004, Earth is suddenly overcome by "spores" launching from an alien mothership. Slowly blocking earth from the sun, in only a week it rains down biological death on the earth... killing most of humanity and larger life forms.

Since then, the few survivors of mankind have sought out each other, and by 2005, enough humanity has joined together to make a stand. Calling themselves the Council of Earth, and working secretly in hidden bases, they must research, recruit and train to the ultimate goal of shooting down UFOs, engaging aliens in combat and reclaiming the Earth from their oppressors and the mutated biology.