During the Black Rebellion we see V.V enter Ashford Academy to see Nunnally. shortly after, while Lelouch is interrogating Cornelia with his Geass C.C becomes aware of this and warns Lelouch. the 2 then leave Tokyo for Kaminejima Island. During this time we see a shot of V.V and Nunnally at the Sword of Akasha with V.V looking board.
2 Years Later when Lelouch had regained his memories Nunnally appears again, appointed as Viceroy of Area 11.
Where was Nunnally that entire time? was she confined by the Geass Order (as V.V was it's director)? was Nunnally aware or made aware of what happened to her?