This episode was very important in finally revealing to the audience what the heck has been going on for the last 19 episodes!! Max begins to develop some tattoos (or runes) on her skin. Somehow it's figured out that these ancient symbols were programmed into her DNA by Father Sandeman. We also learn that Ames White is Sandeman's son, and that he has a brother who is crazy!! It's no wonder with all this breeding cult stuff that's going on!!
It seems the purpose of the breeding cult was to continue producing people who would be immune to this apocalyptic virus that was coming. But Sandeman built Manticore to genetically engineer people to be immune. And it turns out that while his son, Ames, was immune, his other crazy son was not. Hence the development of Manticore to help people who were not naturally immune. So now we find out why Ames has been killing transgenics. And he particularly hates Max because she's the best transgenic of them all.
I found this episode revealing and was definitely glad for all the questions it answered, but I'm still not crazy about this breeding cult storyline for most of S2. I really wish there would have been a S3 where all this was wrapped up and a new story arc had been created.