CupofJoe
Myth Weaver
As long as there is caffeine involved, I am a-o-kay.Thanks to the Cup as what belongs to Joe. Or is it a cup made out of Joe?

Mainly in geography. I needed X to be near to [/far from] Y or for it to take a while to get from A to B.Anyway, thanks for offering up some specifics. If I might take the liberty to re-state: you took the world as-it-is (changing the names to protect the guilty <g>), but then altered ... something. Some sort of weirdness. Did you find those alterations forced "real world" adjustments into the story?
When the big bad appears, everything changes; the current reality, the whole shebang. But even then it was still based on what I had learned.
I cribbed and then tweaked a lot of what the MCs do to stop the BB from what I got from a Demonist friend of mine. And yes, they do believe they can raise and commune with demons [and who am I to judge]. So even a lot of what happened then was "real world". Amped up to 110 rather than just the usual 11 but a demonist reading the story should have been able to follow what was going on and know what I was leaving out or changing.
Neverwhere is probably closer to the mark. The initial hint of something wrong happening is on the first page when as friends are having an end f week drink, someone reads a University newspaper article [it was a few years ago] about an ECR [Early Career Researcher] disappearing. The third in a year. But that was more of a teaser / Pavlov's Gun. I couldn't make the disappearances of scores of people over many years suddenly come to light in Act 3. There had to be a ramp-up and rational explanations along the way. One of the MCs [a librarian] is slowly drawn into a search for "the truth". And as we know people are great at making links and finding patterns, even if none exist...Let me get more specific here. If the story is essentially real-world, when do you let the reader know something is different? A couple of instances come to mind: Folk of the Air, by Peter S. Beagle, and Neverwhen, by Neil Gaiman. In the former, we're a bit into the book before things get weird. In the latter, if memory serves, it happens very early, within a couple of pages. I offer these because in the one, the hook is more with the characters while in the latter the hook is with the plot.
So are the disappearances...
Just coincidence? [These things do happen. Something like 4-5000 people drop off the map in the UK every year]
Is there a serial killer on the loose? If so who? [That guy in the School of Theology looks at people strangely. Or the landowner always complaining about the students destroying their crops? And does anyone else like the night guard in the Physics building?]
Did they just quit, the result of huge pressure of their PhDs [I think a lot of people may be surprised how many researchers have mental health issues during their PhDs. This is the theme I would push further if I was to rewrite the story].
Or is it a demon/old god from another reality using the psychic energy of people at the edge of their sanity to feed? [Seriously? You believe in that crap? For real?]
I tried to keep all the possibilities open as long as I could.
I felt it worked best when I had a Scully/Molder dynamic; a skeptic and a believer fighting to get to the "truth".
One thing I knew I had to do until the final act was reign in the fantasy until the very last moment. I hoped I had dropped enough breadcrumbs for the reader not to be too surprised or felt cheated [far worse a sin]. Almost like an ACD Sherlock Holmes story, I hoped the reader would put it all together and see how it made sense, just as it started to unravel.But that's just one detail. If you have others to offer, regarding how the weird, the fantasy elements, affect the real, I'm all ears. Well, mostly ears. Well, just two, as it turns out.