It's really clear in the ending parts of the game. In Mutation though, the orb and its contents were really transparent. But you can really see -something- (Or more accurately, -someone-) in the later fights with Cubia. To me it appears to be a Kite figure, and I've seen many before me come to that conclusion as well.
And I've only been completing the games several weeks ago. ^_^ Currently have a save file before Corbenik, yay me.
The 'Data never disappears' thing was applied from Mia, though.
Although in GU, there might be a clue to Morganna, seeing how the first trailer had a hidden picture (You probably won't see it unless you go frame-by-frame) of a ginormous eye, which can be seen here:
http://img.photobucket.com/albums/v206/ ... reen07.jpg
Rumour from someone who read .hack//ANALYSIS was that the final form of Corbenik was in fact Morganna directly fused with the Phase. Thus why that picture above was dubbed 'Morganna's Eye' by that person. That title would be highly speculative, if it weren't for the quote "I've waited so long for you to come.", a quote by Morganna from SIGN to be in the second GU trailer... Only said in a man's voice.
Creepy, no?