The Idea Factory - The Failed Experiment
The main character gets abducted by aliens and stuck in a ship alone with someone else. They're informed that humans were created by the aliens and it had been decided that the experiment was a failure. In trying to preserve the data, they were chosen to keep the species going, along with others in other ships. At first, the main thinks it's some kind of prank, but the aliens show the Earth as it's being irradiated and turn off the artificial gravity. When it becomes clear that it's real, the two start trying to make the best of it. Only they're both gay.