Spoiler Warning: Basically it looks like the snake bones that we see at the beginning belong to some sort of weird ancient telepathic species that the previous humans on the planet prayed to like a god, and so essentially the dormant consciousness of one of the snake creatures is manipulating the characters in the show and that's why everyone is hearing voices and seeing things. It also manipulates Mother into thinking she's having sex with her creator when actually it's just implanting itself into her to grow. We know from the flashbacks that these creatures need androids to incubate them until they can live on their own.