UFO: Aftershock follows on directly from one of the endings of its predecessor, where the player agrees to hand over the Earth to the alien scientists who attempt to engineer the planet into a giant living organism. The Council of Earth and their followers take refuge on an orbiting satellite prepared for them by the alien race, but not all the survivors of the original invasion are relocated.

The game starts many years later in their orbital home, with no sign of the aliens and a failing life support system - the player must find out what happened to the Earth and to those who were left behind on its surface, preparing for all manner of surprises along the way.

UFO: Aftershock is a mixture of squad based tactical action and global strategy. The player controls the actions of elite ground troops, alongside the running and construction of an intricate network of interlinking bases from which to operate and expand the tactical maneuvers needed to succeed.

Main features:
- Global strategy intertwined with tactical missions
- Strategic resource and base management
- Advanced tactical SAS (Simultaneous Action System) and RPG system
- Encounters occur inside and outside structures, with a broad range of terrains and multi-level buildings
- Amazing technologies and items to be researched and developed
- All-new system of leveling up and training your troops
- Fearsome new enemies and powerful allies
- Diplomacy - an important strategic element
- Strong storyline
- Destroyable environment