I will highlight some loose ends, maybe this will help us to see a pattern.
We know there was a war against humans, but not what caused it and who they were fighting against.
There is a Virus thats targeting the Y chromossome.
The algorithm was made during The Cascade (maybe it was planed).
There are no human remains to be found from the period everyone was gone.
Superhumans with AI inside them are a thing
Alex doesnt need to eat or breathe, something is sustaining him with what he needs and more, since he is capable of regenerating himself (so he is synthesizing proteins from nothing).
Maybe its just because of the region they're in, but I always found it really interesting how they reinforce again and again that its cold in the summer (something drastically changed the world climate maybe?)
It is said that the demon was mocking mylo, so he has to understand emotions to an extent. (AI? Human? Both?)
If anyone has any idea, please share it if you're confortable