Vincent has become the Proxy and visits the regent.  He learns that he is the creator of Romdo and the people with it.  He appointed Re-l's grandfather as regent when he left and now he kills the man before Re-l's eyes.  Daedelus meets Raul again and he shows him Re-l, another one.  Raul remembers meeting her before but she has grown much since then.  Re-l finds Vincent in the regent's chambers and realizes that the two aspects of Vincent and the Ergo Proxy are not all that there is.  There is a third aspect that has been orchestrating things behind the scenes.