Ah, yeah, Quantum. Lost Eri was pretty damn sexy.
I figured Sophia integrated with Eri's consciousness, making 'Lost Eri'. As for how that scientist got the means to do that, I'm in the dark as well. Stinks, since there was more Quantum could've done. That's what happens when you make a series only three episodes and don't pair it with something to clarify its story like the OVAs with the first four games.