UFO: Aftershock is the second 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 and, unlike its turn-based predecessor, features tactical combat in real-time with pause.

It is the year 2054. Fifty years after the disaster. Fifty years after the surface of Earth became uninhabitable. Retreating to the flying haven of the Laputa the remnants of humankind clung onto existence. Then a revolt against the increasingly rigid and corrupt human leadership of the Laputa escalated into a conflict that destroyed the colony. Now, the remaining survivors flee once again. Can they reclaim the Earth from the unknown forces that chased them into the skies?

After the life support system on the Laputa (orbital space station/city) fails, the peoples of the Laputa revolt against the Human Council, and an armed conflict ensues. As a result, the Laputa's engines explode and the city is destroyed, killing almost everyone on it. The few survivors escape in space shuttles and find another deserted Laputa in space. This Laputa is equipped with a landing pod to Earth, rumored to be long lost. Now you lead the remaining survivors of the Laputa and re-establish contact with Earth and the mysteries within.