So at this point the main open plot points are:
[*]who sent the signal that caused the disruption that led to GAIA self destruct, HADES (and other sub-routines) going rouge and the turning aggresive of machines against humans
- Sylen's actual goals and what he know plans to do with HADES as a captive (while the post credits scene was predictable I'm glad it was foreshadowed in his final dialgue when he noted he'd do it all again just with better precautions - which is clearly what he feels he's done at the end with HADES literally an evil genie trapped in a jar)
Which is a pretty solid foundation for going forward. I hope it doesn't turn out to be Ted (although from characters already established he's the obvious candidate) as that would cut across the plausible backstory presented in Horizon and smack of some of their weak narrative beats from Killzone.
Otherwise pretty much everything else was actually covered and wrapped up enough for clarity:
we know what casued the fall of humanity
we know how the current simplified ecosystem with only subset of plants/animals came into being
we know how the current human tribes came into being
we know the incident that caused the derangement
we know what happened to GAIA, HADES, etc.
we know what happened to Sobeck
we know why APOLLO failed to work allowing for grow of tribal society with no awareness of history or technology
All in all I was very impressed - vs their Killzone narratives - how well ZD hangs together. It's all plausibly presented - a killer robot variant of the "grey goo" doomsday scenario, a reasonably workable desperate final plan to ensure survival of the human race, a reasonably plausible context for why the humans and machines (and the world) is the way we find it at the beginning of the game.
I haven't gathered all logs, etc. but the core seems clear or are there any glaring additional elements not covered?
Also do all the Sobeck corrupted entries decrypt by completion of the game? I've wrapped main quest plus most else but still have a few showing as corrupted and under repair.