The visual novel is a metaphor for severe hikikomorism.
Perceives the outside world and other humans as abominable, duh. The part about how primary attachment and reason to live is a cute girl who may or may not even exist may allude to many hikikomoris' nearly-self-destructive obsession with Moe.
Fuminori sees the world as it really is.
The world is actually covered in eldritch and everything is as Fuminori sees it. Our minds cause us to see a cleaner version to keep us sane, ala self-imposed Platonic Cave. When Fuminori went under experimental brain surgery it broke the part of his brain that protects us and he began to see the world as it really is, anyone who saw Saya saw her as a monster because their brains were not used to something looking like reality should look. When Saya bloomed it returned the world to looking like it should have in the first place. After about a month or so then everyone's minds will readjust and everything will go back to normal
Stan Marsh was experiencing this in the episode "You're Getting Old."
Except instead of Meat-Vision, it was Crap-Vision. If anyone's had it worse than Fuminori, it's Stan. And, of course, as the following episode shows, just drown yourself in alcohol and you'll be fine.