The Doctor jumps around the console and cautions his crew to close their eyes, slamming levers and pushing buttons. The panel closes. The light goes away. The Doctor, Jack, and Rose work, all three in tandem, to shut down the TARDIS. Don't let the unutterable cause you to forget there's a Rift mid-opening, or else you might as well join a cult. The family gets it done, the Doctor thanks them. In the silence, Rose asks what happened to "Margaret." Captain Jack thinks that she was burnt up, a self-execution, but the Doctor knows better. He looks down into her discarded skin-suit, that pile of lies, as Rose asks where she went. The Doctor answers, "She looked into the heart of the TARDIS, and even I don't know how strong that is. And the ship's telepathic -- like I told you, Rose. Gets inside your head. Translates alien languages. Maybe the raw energy can translate all sorts of thoughts..." Maybe it can grant wishes. Maybe it can grant choices. He kneels down to the skin-suit, Rose and Jack huddled behind him, and the Doctor pulls out an egg: "Here she is!" Rose: "She's an egg?" They both are. Grace isn't the end, it's the beginning.
The Doctor exclaims that they can take her home, give her to a different family that might raise her properly. Which, given that their penal system involves turning people into living, screaming soup, seems a bit optimistic to me, but the Doctor knows. "She might be worse," says Jack, and the Doctor reminds him that that's her choice, too -- it always was -- it's still her responsibility to live the life she's been given. "She's an...egg," Rose digests, and remembers Mickey. Nice. She dashes out into Millennium Square.