[[caption-width-right:203: Just so you know: [[labelnote: spoilers]] ''This'' is what keeps the island floating in the sky. [[/labelnote]]]]

Sure it's an adorable game, but it's not so sweet and cuddly beneath the {{art style|Dissonance}}...

* The red flowers that turn mimigas into super strong monsters with no mercy or emotions.
--> "''[[DoesThisRemindYouOfAnything Eat It.]] '''[[RapeIsASpecialKindOfEvil Eat it!]]'''''"
* The broken robot you see right before the fight with [[spoiler: The Core]] stands out (In particular, the obviously frantic command to retreat that they give before they short out for good), as does the [[spoiler: Undead Core with his bloody faces (the big energy ball-spitting form especially)]] and [[spoiler: Ballos' last form, with the corpses.]]
** Also, the blood-red stains on [[spoiler: Ballos' face in his last form]] are [[spoiler: what appear to be ''screaming faces.'']]
** The stage where you fight [[spoiler: Ballos]] is extra creepy as well. There's something to be said for fighting your boss fight on top of a mountain of skeletons, when every powerful slam into the ground kicking up bones everywhere.
** [[spoiler: Ballos' backstory. Poor guy was sentenced to insanity-inducing torture that made him into the maniac he is today. All because he treated his fellow citizens better than his king did.]]
* Post-Waterway [[spoiler:Mimiga Village]], made worse by the music (''especially'' the enhanced re-release versions). [[spoiler:The previously-cheerful village has been turned into a total GhostTown; the only intelligent life that shows up is Professor Booster if you fulfilled a particular [[GuideDangIt obscure requirement]] to keep him alive.]] The same BGM also plays in [[spoiler:Santa's and Chaco's houses.]]
* And then the [[spoiler:revisited Egg Corridor]] immediately afterwards, which cranks the SceneryGorn UpToEleven (especially with [[spoiler:the bloody remains of half-formed Sky Dragons]] littering the place.
* SceneryPorn it may be, but woe betide you if you fall from [[spoiler:the Outer Wall]].
** [[spoiler:''"[[NonStandardGameOver You were never seen again.]]"'']]
*** Bonus points because [[spoiler:the player character never exhibits fall damage over the course of the game, unlike a lot of other robots. So if a fall from the island didn't kill him, he could still be alive, just with broken legs. Watching as the island becomes the base for an invasion of the surface.]]
* Let us look at it this way: say one day you wake up, you don't know where you have been, you just know that you're hurt, you're weak, and you're lost somewhere in this dark damp cave with no memory of anything that happened. You look about and find one exit, and there you find, either monsters, killer robots gone psycho, twisted abominations, or, above all else, [[{{NothingIsScarier}} more darkness with a never ending sense of dread, and no way back]].
* In the Sand Zone, one of the puppies you have to rescue is in a pitch black shack. You have to navigate your way around the [[NothingIsScarier lightless, BGM-free]] interior to get to the puppy, and should you make certain wrong turns, there's a pit with a Sandcroc that's waiting to give you a JumpScare as you land in the pit. The puppy warns you if you get too close to the pit, though.
** It's also slightly better in the re-releases, where the background has been made a dark blue/purple to contrast with the black tiles. While it won't help you if you're in a brightly lit room, [[FridgeBrilliance not that you may be when you play that section]], it does help dampen the maze-like structure.
%% * Once you start going through the last five bosses, everything gets worse and worse. Misery and the Doctor are fine, but then [[spoiler:the Doctor loses control of the Red Crystal and mutates into the Muscle Doctor, a mindless behemoth who charges at you, creates dozens of bats from his hands, and likes to teleport right on top of you. After beating him, his body ''dissolves into blood which ascends past the ceiling''. Next, the blood, which contains the Doctor's consciousness, comes up and plans to exact revenge by mutating Misery and Sue before merging the remnants of himself with a zombified Undead Core. If you don't have two specific items by this, you get to see the entire island crash to the ground, killing everything Momorin and Itoh didn't evacuate. If you do, however... you go through the game's equivalent of hell, where you learn of a wizard named Ballos who was loved by everyone he met, but his jealous king tortured him so severely that he went insane and killed the king, his wife, his child, and almost everyone else he knew. Jenka, his sister, sealed him away, but couldn't kill her own brother. Misery, his niece, forced Ballos to create the Demon Crown and was soon cursed to being forced to follow its wearer. And while you learn this, you fight against demons disguised as angels, robotic bombs, and a gigantic Press. After you learn that last bit of information, you enter the next section to get attacked the moment you step in the middle of the room by something hidden in the ceiling as two invincible spheres called Rolling appear and the demons start infinitely spawning. After beating the boss, it is revealed that is is a giant Press known as the Heavy Press [[TakingYouWithMe who plans to kill you with one last attack]], which is a one hit kill. Avoiding it and following it down the hole it creates, however, gives you another message which states that the Demon Crown can only be destroyed permanently by killing Ballos, which a ghost of puppy asks you to do in the next room. The final room, the Seal Chamber, is filled with bones on the floor that lead to Ballos, who outright asks you to kill him before the four part fight starts, getting more frightening as the humanoid Ballos turns into a giant stone head, then generates eight rock things, then finally reveals ''screaming human faces inside of him''. And after you kill him, the voices of his victims are heard complaining about how hot it is as they try to crush you.]]
* The Core, pictured above, boasting what appears to be nine eyes. [[spoiler:It is also the core of ''the floating island you're on'', and had Misery and the Doctor not chimed in at the last second to [[WhamLine explain what the hell you just did]] and patch up the Core, you would've [[NiceJobBreakingItHero brought the island crashing down to the surface]]. Its undead variant is even worse, periodically opening up to reveal a red, demonic face, or MoreTeethThanTheOsmondFamily.]]
* Did you have Curly with you after [[spoiler:The Core]], but fail to [[spoiler:drain her out]] in the Waterway? The game will happily spring a sudden dialogue box while you're navigating your way through to inform you that [[spoiler:her life functions have ceased.]] It can make you jump if this is your first time going to the Waterway with her but either don't know that this extra step can be done or forgot to do it.
* The bad ending, achieved by [[spoiler:talking to Kazuma in the Outer Wall and accepting his offer to [[ScrewThisImOuttaHere take you off the island to live a peaceful, isolated life with him]]. With you having left the conflict entirely, and Curly either dead or in an amnesiac state, there's nothing left to stop the Doctor from carrying out his plan of raising an army of killer Mimigas. Meanwhile, the screen cuts away to nothing and you're presented with a dialogue box reading "End?" as the haunting bad ending theme plays. [[YouBastard Congrats, you doomed the world by being a coward.]]]]
* The Plus versions include a bonus scenario, the Wind Fortress. In it, [[spoiler:you have to navigate the underbelly of the island with all the risk of falling off the island. After fighting past a guarding wave of Gaudi bugs, you get into an industrialized zone where you encounter Curly copies that attack you relentlessly, to the point of breaking out of replication tubes to lunge wildly at you even without copies of the real Curly's clothes. It all cumulates in a fight with a G-Clone device that is making copies of the real Curly, which will defend itself with a growing army of murderous Curly clones.]]
->'''[[OneHitKill -127]]'''\\
[[SpikesOfDoom You have died.]]\\
Would you like to try again? [[NightmareFuel/CaveStory Yes]] / [[VideoGame/CaveStory No]]