I just read it today. Read the comments too. I don’t think the author is doing anything super crazy.
The academy scenes happened in the past. Mishap happened, and one of the kid or more went berserk and probably merged with the admin robot Meena. The merged result has the face of male MC. All of man-eaters are produced in that facility. And to stop them, our post-apocalyptic MCs need to inject the medicine.
I’d also guess the black-haired male scientist is to be blamed somehow, but redeemed himself by helping some of the kids escaped. He is also the dr who switched bodies with the handsome guy.
The weird ear girl was a precog, and saw the future where our MCs will save/release/kill them because they are monsters now.
These are the predictions based on the usual tropes. Hopefully they are totally wrong.