The surprise/shock of that would be ruined thanks to the internet, unless it only happens to a small subset of players. Things can be tied to the steam-id of the players account and that could be a neat way of "seeding" it. Account numbers that ends in 37 gets the cursed copy, 1 in a 100 chance, then with time that changes from a single digit and it opens to more and more players until everyone is fighting off flesh-turnips with a shovel.
Something like this would also mean that you are intimately familiar with the world and where everything is which turns survival-horror on its head in a very interesting way.
Your idea really got the noggin' joggin' with possibilities. In the initial warm and fuzzy Stardew Valley section of the game you learn to know the townspeople and forge relationships with them, the dating/romance option then turns from considering taking them out on a date to considering splitting their skull open because SOMEONE in the village have a fucking fragment of Ur growing in their brain.
Turns out the real friends were the skeletons you made along the way.
See, what I was thinking is that the game would secretly have two plotlines. The normal one would always be the default one with nothing in-game ever suggesting even the slightest possibility of there being a darker one. Nothing would be creepy, unsettling, or even hint at something much worse being at play at all. All the NPCs would be friendly, normal, non-aggressive, and just as clueless as the player.
The only thing that would be out of place would be the unexpectedly creepy character, and that character would be the only way to ever access the dark game.
I haven't fully fleshed it out yet, but I was thinking the creepy character would be this creepy child that while he does have a loving home with an equally loving guardian, his behavior is bizarre, and unsettling. He would never be violent, or gruesome, or anything like that. He'd just act creepy, and say bizarre, and disturbing things. Some of his behaviors would involve things like wandering alone outside during heavy rainstorms, ending up in places he just shouldn't be able to get to, always being dirty, and appearing emaciated even though his guardian takes care of him very well, his eyes would be huge, and unblinking, and always have a thousand yard stare to them, and he would always be very asocial, quiet, and the few times he did talk, his dialogue would unnerving, and weird.
Like with his behavior, his dialogue would never mention violence, death, or anything like that. It would just weird, and creepy. The best example for what I have in mind is one Meryl's lines from Harvest Moon: Magical Melody.
"I planted...some flowers. While...planting, I forgot about many things."
Vague, creepy, almost nonsensical shit like that. His own dialogue would also never hint to the dark game mode either.
Another thing to note is that he would not important to the normal story at all. You could play the entire main plotline, and never have to interact with him whatsoever. If I was forced to, I might make it so he has one, or two sidequests involving him, but outside of that, the player could act like he didn't exist. The sidequests would also not suggest, nor hint that something much darker was at play.
I'm not what the exact sequence of events would have to be for the dark game to trigger outside of having interacting with the creepy character. This is the part that stumps me.
I do know that once you got to the darker mode, you'd basically just being trying to farm in Silent Hill.
The player character would have to struggle through trying to grow his crops in the poor soil in the foggy, and decaying overworld so that he doesn't starve to death, (there would be a hunger meter, and your character would die if it ran out. Your livestock would all be turned into monsters and/or have just into rotting, unusable carcasses so you wouldn't just be able to use them for free, easy food. All the fish in the river would suffer the same fate so you could no longer fish either.) while trying to hide from the other villagers who have been turned into Silent Hill-esque, Junji Ito-esque monsters who roam around the overworld trying to kill you. If the player had gotten married, and had children, their spouse, and children would also be turned into monsters and trying to kill them.
The player's farm would not be a safe zone, and the now monster villagers can, and will be attracted to the sound of you farming so you'd have to be quick, and quiet about it.
There'd be no weapons in the game, and the only way to fend off the monsters would be by using your farm tools which can break, and become unusable. New tools could be crafted, but only after you learned how to craft them from the books found in the library, NPC houses or ones' purchasable via catalog, or something. In the dark mode, the catalog becomes unusable, and the library, and NPC houses would by inhabited their former owners now turned into terrifying hellbeasts when they're not roaming the overworld trying to find the player.
You'd also need the materials to craft them, and good luck getting them when everything is trying to kill you, and you can barely see more five feet in front of you.
You wouldn't be able to leave the village due to the entire place seemingly being ripped from the ground, and being suspended an unknown, but deadly height in the air, making escape impossible.
Finally, the creepy character would be dead, and the player would just find his corpse lying in the spot where the player character first triggered the event. All the monsters would leave his body alone, and unlike all the other corpses in the game, his would never rot.
I can't think of a way to ever fix what had happened, or why it all even happened in the first place. Personally, I think it's scarier that way.
That's all I have right now.
