The Glitch. It severed chain-of-command and created the Faro Swarm, it lead to the near extinction of life on Earth, and it was anything but an accident. Something about its true nature was so terrible that Liz’s mere mention of going public with its origin cows Ted Faro into submission:
Liz: Or don't sign – and I will make sure they and everyone else on this planet knows the real cause of the glitch.
This raises several questions. Who could have been responsible? Why on God’s Green Earth would they do such a thing? And why were there two instances of the Glitch separated by nearly a thousand years? I spent a long time thinking about this, going through every datapoint in the game. Guerilla had to have left something, some kind of clue to the identities of the ‘Glitchers’. And they did. Dear God they did.
The Datapoint: Dalgaard on FZ answers everything. I’d recommend reading it before continuing reading this post.
So let me explain my theory.
Far Zenith, as the datapoint names them, were a shady "futurist consortium" claiming to include 77 of the world's wealthiest individuals. Now, if that doesn't scream "Evil as F**k" I don't know what does.
In the late 2040's Faro Automated Solutions begins work as a military contractor. At a certain point, it creates the Chariot Line which any sane person can see is a doomsday device just waiting to be triggered. Far Zenith, creates the Glitch that will sever chain of command. Meanwhile, the nations of the world are developing the original Odyssey eventually abandoning it in 2057, leaving the ship a "heap of space junk in graveyard orbit" and its developers all too glad to be rid of it. Far Zenith then publicly steps up and offers to take over, gaining control over the interstellar colony project.
When the Odyssey is near completion, the Glitch is triggered, unleashing the Faro swarm upon the world. Although something happened, Lizzy and Ted found out too much. Probably not the full truth but she found out something, as her threat indicates. Maybe Ted was in bed with FZ or something I’m not sure about this one.
With the Faro Swarm advancing Far Zenith and Zero Dawn cooperate and Far Zenith gets a prototype version of APOLLO (as was always the plan.) Odyssey, with the members of Far Zenith safely aboard, launches, and fakes its destruction. In reality, the members of Far Zenith are simply biding their time in cryosleep until conditions on post-sterilization Earth normalize.
All accept one member: Ted Faro.
You see Ted was recruited probably after the Faro Swarm was unleashed. He has a mission, he has to kill the Alpha’s and delete Zero Dawn’s APOLLO system with his Omega Clearance. This will leave the Zero Dawn humans stupid and dumb. Why you ask?
Because the Odyssey, full of the seeds and zygotes intended for a colony, can be used to re-seed the Earth as Far Zenith sees fit. With the APOLLO education system at hand, they can raise and indoctrinate fresh new generations of humanity, all according to whatever ideals they might have. This was the plan of Far Zenith!
Why HADES was unshackled remains a complete mystery to me, perhaps Far Zenith wanted GAIA out of the way and suspected that she would self-destruct to protect humanity from HADES. They just didn’t count on HADES surviving.