I know what he was looking for originally. Chapter 6/7 spoilers follow:
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When Febronia died, Virgil left her body and went out to eat the brains(?) of the berserk realians. He was doing this to find her consciousness. Sort of like what Joachim was doing when he tried to bring back Sakura from death. He wanted to find her consciousness and put it into MOMO's body. However, we all know that he failed to bring back Sakura. But regardless, I believe that is what Virgil was looking for. He had asked Shion if the realians could share information and whatnot. So he knows about their mental link.
I haven't loaded up the database to check and make sure there wasn't anything conflicting this or supporting it even more, but I had to post this because it started yelling at me. Also, apparently past Virgil acknowledges that there are two Shion's. <_<
Virgil: Dammit. Dammit! Shion!
Shion: What?!
Virgil: Realians can share information, right?
Shion: Yes, they're capable of sharing the information from individual units.
Virgil: Shion's in danger. I have to save her.
Anyway, things are starting to come together for the Chapter 6/7ish area, so I have a feeling I'll be posting something large to explain what I think happened in the real past. But I'm still worried about the Song of Nephilim/Control Code stuff making no sense.