Now that I think back on it, it would seem it was by Morganna's own power, I'm trying to think of a case where a comatose victom got killed in game; Well, by looking at the original games, the closest thing we have would be... having Tsukasa a "Lost One"; because we never see Orca, Sieg, etc. running around in the world after there Data Drained. I assume Tsukasa just simply gets lost in the Network and Morganna had to piece him back together, even while he's being revived we see him.. going through some kind of acid trip, I would assume he's being regenerated from the network fragments.
Or much more likely (since PC death wouldn't shatter your data like that), Morganna was deliberately reaching in there and tearing out the crap she didn't want, thus his memory loss.
This kind of also backs up my theory; because Tsukasa's memories were never revived with his character (Morganna wouldn't want that!) we see the memory fragments appear in IMOQ.
Oooh! My original theory is that Za Warudo itself actually records these memories, but the idea of them being fragments of Tsukasa's is intriguing. I'll take a quick peek to see if there's anything that contradicts the theory.
...
Nope, doesn't work. A good deal of the .hack//Sign flashbacks don't have Tsukasa anywhere near them, so he has no business having them in his memory.