Aftershock is set in a post-apocalyptic 2050 and comes after the events of UFO: Aftermath. The game assumes that the player took up the Reticulans offer of resettling the most able of humanity in a space station, while allowing the rest to die, consumed by the Biomass that the Reticulans could not control (However, in the first game the player could reject their offer, and save the Earth while defending against both the Reticulans and the Biomass). Having lost contact with the Earth, the player must find out what happened.