It doesn't take much thinking about it for the entire premise of the game to become Fridge Horror. Sure, it's mostly a heartwarming tale of a hero saving the girl he loves from the clutches of evil, but the hero in question is a skinless boy who leaves trails of blood wherever he goes, and his adversary is a (possibly aborted, if Edmund McMillen's affinity for the macabre is anything to go by) fetus in a jar who's filled with such hate that he has become an outright sociopath.
A rather subtle one from Super Meat Boy: World 5, The Rapture, takes place in a ruined city. Okay, so far so good. However, a hint of horror creeps in when you realize the likely reason WHY the city is ruined: Dr. Fetus set off a nuke at the end of the last level, though how exactly the blast radius reached the city from Hell is another question entirely. The question of what exactly populated the city is answered when large mounds of Meat Boy-like corpses start showing up, in addition to the Abomination, an enemy that appears to be a horribly mutated and deformed version of our meaty hero. As if that wasn't bad enough, we eventually begin seeing piles of what are undoubtedly large masses of maggots and an already nightmare fuelish monster called a King Carrion. The horror only really peaks, though, when you think about where these horrors are coming from, and especially why you haven't seen any Abominations or corpse piles in a while. If you hadn't figured it out, these huge swarms of flies and maggots are EATING the corpses of the city's residents. And if the name of the level is anything to judge by, you're the only one left...
Have you ever thought about why a skinless boy is looking for a girl made entirely made of bandages? Is he going to rip her apart and wear her skin?