itch.io

Malhar and Isabella were affected by some kind of anomalous effect, maybe the titular "Nihilist Syndrome", derived from a glitch in reality. The protagonist seems to be a computer scientist lecturing about computer memory, and the story places an emphasis on how contaminated data can result from improper memory allocation, causing incorrect behavior in the program, because the program is unable to distinguish between "real" and "false" data. To the computer, it's all real. "It'll run your program with those junk variables exactly as it's programmed to do, even if it destroys itself in the process." Malhar and Isabella were either real students who were contaminated and then erased by this junk data, or they were never real in the first place, solely products of junk data in reality that were then erased by some kind of reality garbage collector.

"Nothing about them was recognizable anymore-just a complete... deconstruction of the body..." By the time the universe gets to erasing them, they've been affected enough that people can no longer recognize them as human. It spreads to the area around them as well, affecting the cleanup process while their bodies are disposed of. People are incapable of reacting to their deaths, as if a mental block prevents them from acknowledging the glitch in reality. It also seems the glitch caused the professor's dwindling lecture attendance.

At the end, it's as if the students never existed. Either an antimemetic effect, or the cleanup made it so they retroactively never existed in the first place, except in the computer scientist's mind.