* [[spoiler:Possessed Zelda]] is terrifying. It's the incongruity between the hideous red eyes and the rest of the body. Bonus points for the resembling that of [[VideoGame/TheLegendOfZeldaMajorasMask another]].
** Special mention to the very moment where [[spoiler:Zelda becomes possessed. She starts writhing in agony despite literally being a hollow shell prior and gets consumed in darkness]]. It's a very chilling scene.
** If Cole had won... [[spoiler:Just ''what'' would Malladus do [[NoYay with Zelda's body?!?]]]] Would he have mutated her? Gone on a nymphomaniacal rampage to spawn a male vessel? Either way, it's uncomfortable to think of.
* Those ever-gasping mouths in the Marine Temple. ''Stop staring!'' And the fact that you have to ram a sword down their throats is equally disturbing in a different manner.
* Like Likes can hide in pots in this game. [[ParanoiaFuel Let that sink in.]]
* [[http://www.youtube.com/watch?v=KlfdA9jfGcA This plays when the rocktites are just out of sight]]. [[http://www.youtube.com/watch?v=e50EpYW_lkQ This plays]] when it is [[AdvancingWallOfDoom stomping closer and closer as you frantically fire ineffectual cannonball after ineffectual cannonball into it.]]
* This unused concept of [[spoiler:the possessed Chancellor Cole]] [[http://www.flickr.com/photos/historyofhyrule/6901261763/in/set-72157629381359715/lightbox/ is quite disturbing.]]
** It's even more disturbing when paired with the description it gets in the Hyrule Historia. The [[spoiler:decapitated Malladus beast head]] begs Link "Please, help me" as it melts, which makes you wonder...is the cry for mercy coming from [[spoiler:Malladus]] or [[spoiler:''Chancellor Cole'', who was unwillingly possessed and mutated]]? He unquestionably deserved his fate but one can't help but feel sorry for him...
* Dark trains. They're giant [[SteamPunk steampunk]] kamikaze trains with creepy flaming faces which patrol areas of the map with the intention of ramming you and exploding. Normally, they would be classified as [[DemonicSpiders Demonic Spiders]], but what truly drives their horror home is their [[PsychoStrings theme song]]. You're driving along, and see one coming up behind you on your map, then, once they come within draw distance and you see how imposing they are, the lovely overworld music is [[JumpScare replaced with a frantic, almost incoherent mess of a song.]] Armoured trains are far worse, While dark trains have the personality of a random number generator trapped in a hockey arena, Armoured Trains actively pursue you[[WantonAbuseOfTheCommonComma ,]] even going as far as to change direction, and even try to sneak up on you. And there's nothing more startling than to be chasing down trains in the Endgame, only to have that last one turn around and rocket down the tracks at you at five times it's normal speed just as your tear of light wears out.
** The fact that the first encounter you have with them has a huge chance of them sandwhiching you? Sleep with the image of two demonic trains coming from ahead and behind, and you being as vulnerable as a princess because you took the wrong route.
* Cole subtly revealing his true nature after Link's ceremony at the beginning of the game is undeniably creepy.
* The Forest Realm. What's with the creepy music and gloomy scenery. The moment you enter, you will wonder if your game has transformed into some kind of jump scare game. Heck, even Zelda lampshades it.
--> Zelda: The forest was so creepy, I thought a ghost might pop out, Scary!
* While minor, as well as hard to notice, in Fraaz's death scene it has lost control of its magic. How can you tell? It appears to be thrashing around, and its vocalizations make it sound like it's distressed. Just imagine if your body bloated up without your control, knowing why it's doing that but being unable to stop it.