When Helo shot Athena, the mother of the next race of sentient beings, and she downloaded on the Resurrection Ship, Caprica was there. To greet her, this third hero; not a Hero of the Cylon but a woman drowning in oceans of memory, who had been hurt by human and Cylon alike as much as Caprica or Boomer ever had, and still committed herself to bridging gaps. And simply in the look on her sister's face, Caprica knew her time on the Baseship was done. You never run from anything immortal, because it gets their attention, because their existence deforms the universe and our worlds merely turn around them. She snapped poor Boomer's neck, the false mother, to save the child; she escorted Athena and Hera back to the Fleet, her stomach turning over and heart racing, and stood in the scariest place in the universe, wondering whether they'd murder her. And back with the Cylons, her sister Natalie took her place.
She was manipulated in the brig by Laura Roslin, and learned to hate her; eventually she began to share her dreams: taking Hera to see the Final Five, in the truth of the Opera House. She never knew Gaius had had those same dreams and visions, long ago. Roslin took a crack at her programming, daring her to remember the Final Five. To remember that mother's love. She was visited by lonely, sad old Saul Tigh, who told her she'd never see Hera again. He looked older than her, but he was only a boy. He'd only had one false life, and she'd had ten thousand, every single one of those days directed toward one goal: purity and beauty, as cold and savage and bright and lovely as the forest cathedrals she projected on the world. Another green world, untouched by pain and history, ready to begin with something new.