Dr. Mephi is behind Sonmi's release from Papa Song's. He takes her to Taemosan University and puts her in the care (we use that term loosely) of the incompetent Boom-Sook Kim. When he sees Sonmi's potential, and Boom-Sook's dangerous treatment of her, he takes her from Boom-Sook and starts her down the path toward becoming the figurehead of the Union rebellion.
In the brief time we see him before his execution by Unanimity, he introduces Sonmi to a new way of thinking, telling her things that she at first deems blasphemous and deviant. He says, "Try this for deviancy: Fabricants are mirrors held up to purebloods' consciences; what purebloods see reflected there sickens them. So they blame you for holding up the mirror" (5.1.256). What he says his true, but he also has another point: to talk Sonmi over to his cause. Does Mephi free Sonmi, or is he just a different kind of master, using her for a different purpose?