The visual novel is a metaphor for severe hikikomori.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.
Saya is a clone of one of Kimbery's joutenSpecifically, the jouten corresponding to All-Devouring Depths Shintai, aka psuedo-shoggoth with acid tears. What Ougai opened was actually a portal into an Infernal's lab where he was working on creating ways to terraform Creation into something suitable for the Reclamation, and drew the immature behemoth-clone of the All-Devouring Depths jouten into the game's Earth. Unfortunately, the Infernal noticed and followed, and decided to turn the planet into a testing ground for the future Saya, inspiring a parental instinct in Ougai and activating Saya's intincts to mimic her original and become a mom ASAP. Since Saya was truly female (unlike true Yozis), she could not impregnate people with Kimbery's colonists, but instinctively knew how to shred the minds of people who saw her through UMI to avoid detection while she sampled biomass (this is why she finds prepared food horrible-without biometrics, it's just DNA, which a being spliced off from another which essentially is a primordial soup, is just plain unneeded). That was, until she met Fuminori. The reason the brain surgery was "experimental" was that it wasn't technology at all, but a bit of thaumaturgy Saya's Infernal "father" invented to twist Fumiori's (judged an ideal subject due to his ability to remain isolated without setting off too many alarm bells) perceptions to be identical to Kimbery's, who being Kimbery, naturally sees the world without her touch as horrifying and wrong, while Saya is seen as a younger version of Kimbery's human form. Using her naturally divine beauty when viewed as another human and literally being born with an instinctual knowledge of how to use her feminine wiles to find a suitable mate, she seduces Fumiori and quickly turns him into her library on human biology / concubine. Her powers come to advance very quickly afterward, as she learns to Desecrate life forms into Kimbery's ideal (ie, mutant, often amphibious sea life). Depending on the ending, the experiment fails as the procedure is undone and Saya is forced to relocate, it fails utterly as she ends up being frozen and, not being a spirit, is not able to unfreeze, or is a resounding success as she completes her analysis of the planet's biosphere and develops a terraforming agent that quickly transforms the world into Kimbery's idea of paradise-a watery world of tentacled coral reefs, warped Kaiju, and glass cities overlooking green-blue bays filled with monsters. After Ryoko dies, the Infernal sends a colony fleet of demons to assimilate the reborn world into a new empire, and collect data to be used on Creation. This makes it even more Nightmare Fuel, because Desecration effects don't warp minds. Which means that Saya's victims are still fully human, mentally, even though their bodies resemble something out of the Mariana Trench. Then their Great Mother's direct lieutenants arrive to collect in full the debt they acquired from the "miraculous gift" they were loaned.
Professor Ougai was suffering from the same disorder that Fuminori hasGiven that he kept her in his house while he was studying her and was never freaked out by her appearance, it makes sense. How long did he have it? I don't know. He may have been much more high-functioning than Fuminori, however.
Fuminori's perspective is partially a result of seeing his parents' deathIt was mentioned that the death of Fuminori's parents was so grisly, it was difficult to tell their corpses apart.
Urobutcher had the same experience as Sakisaka; this show is practically his autobiography.In an interview he stated that he nearly died in an epidemic and developed "eyesight of the dead" while in the hospital; hence his extremely Darker and Edgier worldview. Somehow his illness caused him to literally start seeing Sakisaka's vision of a world of gore. They say to write what you know...
Saya is a magical girl.Or a witch.