Fuck it I'm going to make a wild theory. First let's go over what we know (or suspect)
1) I still think the school is in the past since Tokio is probably pregnant and I think Maru's her son
2) Some time after the school an apocalypse happened killing most people on earth
3) People are infected with man-eater disease including random people like the king of hotels
4) Inside the school the kids are likely some kind of artificial life turned human for the sake of some experiment and are (despite being made to be super human and immune to all diseases) dying from a mystery disease
5) Inside the school the AI seems to want the kids to breed and escape
6) Maru has the power to kill man eaters and perhaps the infection that causes people to transform(at the very least he can sense it)
7) The person who taught him how to do this has given him a serum that he is supposed to inject his mom with to save the world, in a place referred to as heaven
Alright here we go
Around the time of Maru's birth there is some sort of incident(likely an escape attempt caused by Mina at the school
As a result Tokio somehow creates or becomes the vector for the man-eater disease which spreads across the world but somehow gets her stuck at the school while the other kids escape with Maru
Some of the escaped kids or their allies keep track of Maru and discover the he's basically the antidote to his mom's plague so use him to make a vaccine which if given to his mom will spread over the world
Ok that's what I got for now. Also I think instead of the infected girl from this episode being from the school, I think it was the doctor. One because she seems a bit young. Two a super genius around the right age with knowledge of man-eater stuff and a school related symbol it just seems more likely.