There's a reason why this game is compared to Majora's Mask in terms on how dark it is.
In Twilight Princess, you find out that the Cthulhu-like Shadow Beasts have attacked and transformed villagers into them. You get to learn about it from the perspective of villagers living in constant fear of the same thing happening to them. The knowledge that the monsters you are fighting were once living people is horribly unsettling.
Barnes: How long do you think we can hold this sanctuary against beasts that strong, huh? Once they attack, it's OVER! Remember the lady from the general store? Just one of those things attacked her, and a whole gang from town went to save her! And what happened? She was already gone,and there were TWO monsters waitin'!
The bird twilight monsters. They look liked they have had their heads blown apart by an explosive or a shotgun. They also have these hideous cries and are quite annoying to fight. And in the Twilight Palace, there is an outside section where they are flying all over the place.
One of the worst Redeads came in Twilight Princess: Giant, mummified scarecrows with red scarves around their necks with giant, hollow eyes, shambling about as they drag a sword-cleaver that would make Pyramid Head proud. If they see you, they instantly shriek a hideous banshee scream that paralyzes you instantly. Then, they shamble towards you, and when in range, cleave their swords into you, taking a good chunk of your health. And what makes it even worse is that you are paralyzed until you are hit or it wears off, and it almost never wears off before you are hit. Heaven help you if you are in a tight room with FIVE of them, cause then you get at least two going after you at once.
There is one point in the Arbiter's Grounds where it's possible to be paralyzed by a Redead's scream while you are standing on quicksand. Watching Link sink to his death while paralyzed is arguably worse than watching him get whacked by a Redead's sword.
The Redeads in Twilight Princess actually look more like Redead-Gibdo hybrids. They have the eyes of Redeads, and the scream, but they're also mummy-creatures with bandages drapped all over. That red scarf thing actually looks more like blood soaked bandages whenever one sees them on a TV screen, as opposed to cloth when viewing a still image◊.
That would be because they were intended to be Gibdos (and still are in the Japanese version). The Redead label seems to have been a translation mix-up.
Armogohma in Twilight Princess is the largest and most realistic-looking Gohma yet seen in the series, and as such is an arachnophobe's worst nightmare.
So, you're playing Twilight Princess, and you're in some damn dungeon or another. You're having a good time, whacking things with your sword and finding keys, when suddenly, you hear a faint squeaking. And you're not moving as fast as you normally do. So, you go into sense mode and see that you're covered in ghost rats.
What's even worse is when you see Midna start to freak out while you're in wolf form. For a character that spends most of the game ordering you around and making snarky remarks, seeing her scared tips you off that something very bad that you can't see is happening. (most people thought that was a glitch)
So you see a treasure chest on the other side of a quicksand pit and decide to wade across, no problem. But on the way back hundreds of bugs swarm out of the walls to latching on to Link to make him cross slower and sink faster. At least you can see the the scarabs unassisted.
Speaking of Midna, how about her happy look when she takes out the fused shadow after Zant transformed her? Part carnivore, part demented gaping mouth is the best way to describe it. Some expected a Face-Heel Turn from her at some point in the game and that part did not quell those worries.
Midna turning into your friends and screaming in terror in order to convince you to be her servant. Fortunately, she becomes nicer, but a lot of those early scenes with her are just plain creepy.
The fact that it obviously scares Link is pretty disturbing. This is the guy who's already faced unimaginable horrors, with many more to come, and he actually falls to his knees, shocked and overwhelmed, when it ends.
What makes it especially nightmarish is that it's completely dissonant with the rest of the game. The series is no stranger to nightmare fuel, as these entries show, but this one made absolutely no sense. It's as though they were like "Backstories are boring, let's spice it up by explaining it with the most unsettling visuals a T rating will allow."
It's Surreal Horror from a meta perspective as well. Just before those eyes show up, the camera pans down to reveal Ilia, Link's childhood friend, is holding a knife, with which she stabs the fourth wall. This is a freaking Zelda game. The resident Damsel in Distress is not supposed to be trying to kill us. That is not how it works.
Additionally, the off-camera sounds, plus her knife falling away, plus Link suddenly standing alone and charging toward the Triforce... yeah, Link was quicker on the draw and killed Ilia first.
How about that hand that chases after you in the Palace of Twilight? When it gets close to you this suspenseful music starts to play but you make out the door so no problem. You casually walk through the next room and the hand comes flying through the wall!
Skulltulas. Fricking Skulltulas! Unlike Ocarina of Time, these Skulltulas move around like real spiders.
Encountered your first Skulltula, your reaction may change from something of a "Wow, they did an amazing job of fleshing their look out" or "Heck those are pretty creepy", all seemed fine and dandy till you got closer and instead of it showing you its belly side, it CRAWLS OFF ITS THREAD AND COMES AFTER YOU! The reaction may be something of a "THAT'S NOT OKAY!!"
Even worse, right before it happens you can see her head twitching erratically in the reflection with her moaning. Seriously bad things are about to happen.
Fridge Horror happens once you realize that this is the same yeti you've been asking for directions that whole entire time. So, the player has been literally interacting with the enemy boss that whole time before said battle. It was also a bit unsettling once after you retrieve the boss key and head out the door, she appears out of nowhere saying that she finally remembered where the mirror piece was.
Actually she knew all along where the mirror piece was she just couldn't remember where she put the key.
Seeing all of the frozen Zoras in Zora's domain, it's just eerie.
Consider also that to thaw them, you drop a HUGE CHUNK OF VOLCANIC ROCK on the ice in the throne room. Granted, you had to do it, but how many Zoras were killed on contact with it, and how many by being flung against something by the explosive gush of water?
Zant easily qualifies due to his insanity alone, but what really gets him here is his very, very, very disturbing confrontation with Midna right after you complete the Lakebed Temple, forcibly holding her in place and whispering "I need you" in her ear as he's drooling, then blasting her with Lanayru's light beam attack, which nearly kills her.
The fight against Zant is both hilarious and creepy. Before the fight even starts, he has a Villainous Breakdown and starts going nuts, screaming and moving like a maniac. Then the fight starts, and gets progressively intense as Zant gets crazier, until the final phase where he goes fucking apeshit and attacks you madly. The music also gets faster and crazer as the fight goes on. Finally, when you kick his ass, the way Midna finishes him off is the icing on the scary cake.
To really drive it home? Even Midna is utterly horrified when she realizes that she popped Zant like a zit with just a fraction of the Fused Shadows' power.
The scariest part of all this is how much is clashes with Zant's personality beforehand. In the earlier parts of the game, Zant was incredibly collected and intimidating, possessing a degree of subtlety to him that no other Zelda villain has been able to reach. Then he just snaps.
The bug collector, Agitha, can qualify as this. If you have a bug and don't give her it during her dialogue, she says "I know you have bugs" as you leave and audibly growls.
When you keep in mind that the boss of the second dungeon, Fyrus, is Darbus, a sentient being with hopes and dreams and compassion, corrupted by the Fused Shadow, itís very disturbing. The way he's been futilely chained up is like something from an R-rated exorcism movie. When you defeat him and take the Fused Shadow, it's chilling to think that you're gathering artifacts that can completely overpower a proud Goron elder like that.
Same can be said for the Ice Temple's boss, Blizzeta, a female yeti who also had dreams and a husband before finding that haunted mirror piece. (See above)
Thankfully — to some degree — the other bosses seem to be made wholly of a Piece of Heart and either a Plot Coupon (Diababa, Morpheel, Armogohma, and Argorok) or a dead skull plus magic (Stallord), rather than corrupting a sentient being.
The fight with Puppet Zelda can be rather unsettling. It's mainly because you're hearing Ganondorf's voice coming out of her, and the Demonic Possession in general.
The first Skull Kid chase on the way to the Sacred Grove is likely to send some slimy shivers down a first-time-player's spine, what with the endless packs of insane looking, grinning puppets constantly lunging at you, and the nostalgic yet depressing version of Saria's Song playing in the background. It's even more terrifying when you realize that the puppets are created by the Skull Kid blowing into his eerie sounding trumpet, which he plays along to the BGM.
More of a creepy example than anything, but going on into the middle of Lake Hylia and turning on the Wolf senses can be very unsettling. Just darkness... darkness... darkness... and more darkness. And some sparkly water but, it's just so dark.
The boss of the Lakebed temple, Morpheel. It starts out in a fashion similar to the boss of the Water Temple from Ocarina of Time but then the second phase begins You have to fight a giant lamprey-like creature. But that's not the worst of it. To attack him, you have to Clawshot onto his back, then you have to stab him repeatedly in the eye! Complete with blood spray! And upon his death, what do you see? A lovely view of his empty eye socket! Thanks a whole lot, Nintendo.
As a person with an intense repulsion bordering on phobia of drowning, this troper can tell you that the slow, eerie and macroscopic descent to the lakebed floor where Morpheel lives was NOT pleasant. Majora's Mask had the idea first, but still.
Best Boss Ever it may be, but Argorok definitely counts as you go through the City in the Sky. You know it's gonna be the boss and even veteran Zelda players playing it for the first time will just be expecting it to be at the boss room waiting for you. Then you cross a bridge, a cutscene is triggered and Argorok sweeps down out of nowhere and destroys the bridge you just crossed. This can be some serious Paranoia Fuel as it can keep players on edge thinking it could come at them at any moment. And if you're at a high enough place and use the Hawkeye to look at the highest point of Celestia, you can actually see it flying around the tower showing that it could, in fact, come after you at any moment.