 A large portion of the episode was based on the ancient astronaut theory , which proposes that intelligent extraterrestrial beings have visited Earth in antiquity or prehistory and made contact with humans . Frank Spotnitz later remarked that he was <unk> at how little negative fan mail the show received , despite the fact that the " Biogenesis " / " The Sixth Extinction " / " Amor Fati " story arc heavily hinted that aliens were the <unk> of the notion of God and religion . He credited the manner in which the show handled this delicate subject , saying , " Often in the past , we 've done stuff where I was sure we would get angry letters . But we rarely do . And the reason is because of the way we handle things . In ' Amor Fati ' we treated the religious side with respect . " The ancient astronaut themes were later revisited in the two season nine episodes " <unk> " and " Providence . " 
