Twelve months ago and John's provided Ellen with a black t-shirt and pants. He laughs at her, his perfect wonderful mother: "I've often wondered what changes the mortal experience would have on you. I never seriously considered the answer would be virtually none!" she asks him about his nightmares, those troublesome missives from a soul he forgot, the other half of the universe that grows ever more powerful when he denounces it: "Do you still suffer from night sweats? And scary dreams of dog-faced boys, chasing you through the yellow mists?" She's an artist. Any real writer could tell you exactly what she means: the half-beast from Howards End, chasing Monk Cavil toward the brink, daring him to complete the equation. To stop pretending you have the option of being half a thing, when your soul demands your other half in dreams and yellow mists. In his current configuration, it's in the best interest of "Cavil" to ignore this most obvious of dreams, but Ellen knows better. Every word's a spell.
"Sleep. That's a good example of a supremely unproductive human attribute that for some reason you chose to write into our software. Fortunately, I was able to delete that particular subroutine. And I stopped sleeping about twenty years ago." When you can do whatever you like with your programming, that's fine. I won't cry out that he's forgotten how to dream, I'm sure he's fine. But that means for twenty years at least, he hated dreaming. He refused those messages from God. And now he doesn't hear them, just like he wants. Because they were too hard, and too confusing, and too scary for him to alchemize. So he worked on other people.
"If you really think we poisoned you and your siblings with human traits like sleep," Ellen sighs, setting up this half of the episode, "And Centurion values like belief in a living God, why then did you spend all these years in single-minded pursuit of such human ideas as vengeance and murder? Why not just choose to explore this notion of being the best machines the universe has ever known?" Because he's not one. Because sleep or not, those dog-faced boys keep pulling at him. But that's not something he can see yet: "Because justice pulls me back. My forebears -- on the Centurion side of the family -- were the slaves of humanity. And I want justice for that." She's sad, and he's lying, but she tells him it doesn't have to be this way, and he ignores her.
When Boomer enters, their fight goes from subtext rapidly to text. He smiles and tells her to put their lunch platter down; Ellen greets her as a person, as a person with a viewpoint ("Boomer! I can't tell you how good it is to see another person I know! I'm assuming there's a whole ship full of my children out beyond the guards..."); Boomer only stares. She's been here since (I think) being killed by Caprica and Athena, since Hera was stolen back and her purpose with it; she's at her worst, her most vulnerable, her least vulnerable. She is a machine; she only stares. John laughs, and tells her to say hello to God.