What is the main conflict in Children of God: A Novel by Mary Doria Russell?

Children of God takes up the story of Emilio Sandoz as he heals from the ordeal that he suffers in Mary Doria Russell's first novel, The Sparrow. Emilio is shanghaied back to the planet Rakhat, where he had been mutilated and gang raped, because this serves the interests of Vatican and Jesuits. On Rakhat, he sees that the political situation has changed and he moves to ward off the extinction of the formerly dominant and tyrannical species.