Ok, at this point, I have no clue where the clues are. I did all of Emit's opportunities that I could get and couldn't really find anything in them. I may have missed something, but I tried to read it all as thoroughly as I could. There is one opportunity chain that I got on a previous playthrough involving bot building, but I couldn't seem to get it to come up this time around. Maybe, the clue is in that chain of opportunities. It was the chain that involves buying a plumbot at one point. My guess would be that nanites are somehow involved in what happened, especially since they're mostly found in the wasteland.