Wow! This is amazing! Of course only for people who have finished the game.
But I was hoping that someone would put together a Timeline of Events for the game and lo and behold it is done
But mean, reading things chronologically really hits home just how literally fucked the people in Pathos-II were. There seemed to be little coordination across the sub-complexes and especially the lack of anyone knowing what happened to anyone in The Abyss (pretty much abandoning everyone at Tau).
For me, it also doesn't paint the Warden in a good light. Given how fast things deteriorated after the Comet, it definitely seems the WAU actively coordinated to sabotage and make life as difficult as possible for the survivors. The only way its actions make sense is if it was logically certain that transferring brain scans to machines was the only way for humanity to survive and that it also believed somewhat in Sarang's "Continuity" logic and killed the originals.
EDIT: Now after watching all the live-action Transmissions, I'm doubly sure that the Warden was trying to manipulate the Pathos staff into being "transformed" by the structure gel. In it's programming, I could see it having decided that given how it is now seemingly "rewiring" the ecosystem in order to preserve humanity, it needed to ensure that these humans be "rewired" as well.