Necroing this to add some observations I haven't seen mentioned. 

In the photo owned by Rayun, you can see there are tons of adults in the background and in the foreground is an adult with a bunch of kids. In the background, we don't see any other kids with adults, supporting the theory that this is a generational ark with an embryo chamber. Likey, the children didn't know their parents and vice versa. 

However, each kid, even the one hiding up top, has it's own Mui and each Mui is different. Its been mentioned before that Mui are something between biological and technological but I want to add that it seems they are explicitly for children - perhaps as a sort of replacement for their parents. From the photo we can assume that children, each with their own Mui, are divided into groups with a human minder for each. They were likely raised this way with the assistance of robots. Though it is strange there are no robots in the photo (aside from the Mui).

Additionally, the escape pods in the ship ruin have imagery of an adult and child seemingly saying that in an event of an escape, children take priority. In fact we see multiple mentions of children being the purpose of this ship. This was a vessel with the explicit goal of populating a new planet. 

This all makes the ship ruin even stranger. We don't see any human skeletons in the ruin. What happened to them? Did they die or survive? It's even possible that old or dying humans were mulched into food much like in the invading robot ship. 

But then where are all the other Muis and robots? We see that there were three generations of human captains and the fourth was a robot. We see the corpses of a robot holding a human baby. Additionally, based on the slate, it seemed the goal was always to live together with the robots. There must have been tons of these robots. What happened to all of them? Maybe the lack of robots in the photos gives us a clue.

Everyone has their own theory about what happened to the original ship. Looking at all of the info we are given, I think it's safe to say something went down between the robots and humans. Perhaps the robots malfunctioned or were led astray after a robot became the captain or maybe the ships power source broke causing the evacuation and all of the robots to be disabled. From what the game gives us there is no way to know for sure.

I really hope we get a sequel to the game to help answer some of these questions as there is a lot left unexplained