UFO: Afterlight takes us to Mars, where a human colony has been built with the help of the Reticulans not long before the events of UFO: Aftershock took place. The Martian base is self-sustainable and provides all the necessities for the survival of humans on a foreign planet, mainly breathable air, water and food. Although the people inhabiting this colony have the technologies and knowledge required for their further development, basic survival is their major concern. Their only activity is research of a nearby excavation site, which proves the existence of an ancient, intelligent and highly developed alien civilization.