We soon find out that V.V. gave to him a Geass that allows to rescribe different memories in the mind of who he wants. He uses it with Lelouch, when Suzaku took him in front of him.
In the past, he made a contract with V.V. and their goal is to kill gods. They seem to be very tied and he calls V.V. "nii-san" (in English big brother).
Nowadays, he's using Nunnally, and he didn't told her about Zero's true identity.