ILLTALE is a AU mostly focused in being a "What if...", in this case. A "What if using the six human souls powers actually backfired?" Boom, ILLTALE has been born!
The human hadn't fallen into the Underground yet... For now, everything was at peace and calm. At Alphys' LAB, Alphys had just finished an artefact/invention called Chrono-01Vision. Its abbreviation would be C-01V, an artefact capable of letting the user briefly see the future by consuming some power of the CORE. Alphys eventually used it to test its functionality. Everything was going well until she caught a glimpse of something terrifying. Alphys had seen how a human would eventually fall into the Underground and start a genocide route. Alphys didn't take long to quickly start panicking and trying to find a way to prevent this all as fast as she could. Alphys, of course, didn't take long before letting the King of Monsters, Asgore Dreemurr, know about this, telling Asgore that a possible way to save monsterkind was to use the power of the six human souls. Asgore at first hesitated, as he always planned to reunite the souls to eventually break the barrier... But what would be the point of not using the souls now while they have the opportunity? Breaking the barrier would be pointless since they would die first because of the human, so Asgore eventually agreed and let Alphys have access to all six human souls so she could run her urgent, last-resort alternative. Eventually, Alphys introduced the six human souls into a machine designed to extract vast amounts of power, adding some extras like leftover artificial determination from her past experiments and the soul of a monster. Alphys planned to use the six human souls as a massive power source, extracting their energy and distributing it in small amounts throughout monsterkind, hoping to strengthen every monster rather than concentrating all the power into a single being, The experiment had a 60% chance of succeeding, even if the chance was still not guaranteed and there was still a risk of the alternative going terribly wrong. Alphys decided to gamble on it and start the process of extracting power and energy. It's not possible for it to end wrongly now that the chances of success are higher... right? It turns out that, at a not very appropriate moment, a peculiar flower had noticed Alphys' desperate alternative... FLOWEY... FLOWEY had overheard Alphys and Asgore's conversation and secretly spied on them. Out of immense boredom and a craving for something new, (Reference?) FLOWEY sabotaged the machine by attacking it with vines and pellets, causing it to malfunction, draining a large amount of the souls' power and leaving them weakened. The six human souls and the extras, the leftover artificial determination extract along with the monster soul, which were supposed to provide extra power, ended up mixing with the weakened human souls, which was definitely NOT supposed to happen, creating purplish mist and puddles that quickly spread out from the LAB and eventually infected the CORE...
All of this happened while the human was still absent...
Infection born from Alphys' failed attempt to save monsterkind, a dangerous infection that focuses primarily on attacking and corroding flesh, tissue, and overall organic matter, killing weaker monsters, leaving flesh rotten or decomposed in monsters considered bosses or with higher stats (Toriel, Asgore, Undyne, etc.), or, if luck is not by your side, turning you into a deformed amalgam.
[UNIVERSE DATA: FUN value: 66
Genocidal route streak: 0]
Original Undertale & Characters by: Toby Fox!
So no, Timmy, Sans and Papyrus aren't completely immune because of possible favoritism. The infection literally had to find another way to affect them.