The story is situated on Mars. It starts where UFO: Aftermath left off and runs simultaneously with UFO: Aftershock. While the Laputans on Earth are fighting Wargots and Starghosts and finding out what caused the destruction of their home planet, a small colony on Mars is trying to survive and flourish.

The player will gain more details about the activities of intergalactic organisms, called Myrmecols, in the solar system. The scientific research and communication with different factions on the Earth gives him a different perspective on the events of the two previous sequels. In UFO: Afterlight, the players will meet with brand new technologies, unusual environment and enemies both old and unknown.