Aight for people who need a refresher on the plot the current mc is just a save file of the real makoto who created the virtual ark in order to bring back the love of his life who ended up dying in an accident. The problem is that her real brain is still functioning albeit damaged while the ai we see is merely an incomplete copy on the ark made from whatever fragments of her that could be harvested. So her brain is in a torturous state of disorder forced to continue living in a jar while holding some form of sentience as the original makoto went on the ark to get some virtual Incomplete puss while the real ai suffers. As for the overall problem for the other billions of people, because of the original makoto’s choice, he’s basically moving the virtual earth to a previous save point while making different decisions which will inevitably ripple through all other actions thus changing who will be born or who dies etc. causing those left out to be stuck in a black void.
"Your current self should be capable of doing what your future self did."
Yeah no, that isn't really how it works. There's things like different motivations driving someone, experience accumulating and sometimes just the factor of dumb luck leading to breakthoughs.