The wording of "cognitively contaminated" from last chapter sounds to me like once your brain is infected, the actual physical parasite doesn't really matter and you're doomed no matter what. It's literally and figuratively a "brain worm" that's just going to remanifest itself.
The “cognitive contamination” and the parasite are separate coexisting phenomena. The “cognitive contamination” is just the fact that you see things differently, and your brain smoothes over any cognitive dissonances like the entire school being so blasé about a girl slicing her best friend‘s neck open. The parasite only infects exceptional people, or it infects people and they become exceptional, or they infect people who are perceived to be exceptional. The cognitive contamination allows the parasite to thrive undetected.
The fat man was another coexisting phenomena, in that you can live a long life whilst infected by the parasite (the old man who was infected but stayed in the village) but now that he no longer exists what will happen to those sent through the tunnel.
My thinking is that either the scientist or baseball boy have now become the oni in the mountain that’ll eat the infected. The wound in the Fat Man’s abdomen definitely looked like someone cut out a nice hunk of monster steak to munch on. Just like the old man who ate the oni in the original myth.