The big question that remains is, the glitch that woke up HADES/sent it haywire/led to all this was said to have come from an unknown outside origin. What could that possibly be? the only people, groups, or culture with advanced enough computer technology to understand the system, much less hack or interfere with it, was old-world. We don't know exactly what all is out there, since the game covers a very small area, but it doesn't seem too likely that there's a tribe or shaman of this world that did it, unless they found old technology that they could awaken - but what old tech would that even be? Nor do I think Sylens had anything to do with it, since he couldn't even get into a lot of the more secure ruins, much less compute with them.
(Side question, wtf is up with Sylens at the end and leading into the sequel, anyway?)
Unrelated, my girlfriend read a forehead-smacking revelation that I also had somehow missed. It didn't escape my notice that there was some Egyptian theming going on with machine names - Khopesh, Scarab, and Horus; as Zero Day approached, Ted went into lockdown in his own "pyramid" in Thebes, too. Nor did it escape my notice that triangles were a big motif for Ted's company, although I somehow completely failed to put 2 and 2 together and realize, duh, they're not triangles, they're pyramids. That's not the "oh god dammit" one, though. The "oh god dammit" one is that Faro sounds like Pharoah. Can't fuckin' believe I missed that. I mean, that's the whole point of it all.
Anyway, that wasn't unrelated at all, because if Faro has this obsession with ancient Egypt and sees himself as a Pharoah, he's probably tried to "mummify" himself somehow. Maybe that's preserved in the afterlife, but I wouldn't be surprised if he uploaded himself. Or, one other possibility, Sylens mentions offhandedly that one of the technologies the old world had was cryogenics - mummification may involve having literally preserved himself.
I mean, he seems like an obvious candidate, gigantic piece of shit that he is. (I almost hope it's him because I would very much enjoy killing him.) But also, I'm not sure what motive he would really have. Even when he wiped Apollo (that absolute motherfucker), he did so in the ostensible hope that the reborn future would live better lives and not repeat their (his) mistakes (lol what an idiot). And he always did seem truly regretful at how horribly he had fucked up. I don't know why now, he would decide that he'd rather reactivate HADES and burn it all back down to the ground. I mean, I guess 1000 years of being an AI or unfreezing can "drive someone crazy" or something but that feels cheap. Another AI? Aliens? The Texan asshole ? I dunno, I'm sure the sequel will explore that more, even if not entirely conclusively.