The very first scene has Link's nightmare of Ganondorf, with his very loud theme playing as he stares down at Link with an evil grin.
The Final Battle. Just when you think Link and Zelda have won, what with Ganondorf getting a No-Holds-Barred Beatdown from Link beforehand and having his entire castle come crashing down on him, you hear a strange noise. Link goes to investigate only for a ring of fire to surround the area and thus, blocking him off from Zelda. Then, Ganondorf's mangled, beaten body bursts out of the wreckage of his castle, with an expression of anger so chilling it could send fear into anyone's soul, his eyes lit with a bright, yellow glow, all while panting heavily. Then he shows the Triforce of Power glowing on his clenched fist. Cue him roaring like a beast and transforming into a horrifying, boar-like abomination wreathed in shadows, complete with two absolutely massive blades which alone dwarf Link himself in size. And just before Link can attack, he knocks the Master Sword right out of his hand and right beyond the ring of fire, with a ominous droning theme playing during this final, seemingly hopeless battle between good and evil.
And in one branch of the timeline, Link lost.note Specifically, this refers to the branch of the timeline leading to A Link to the Past... and the original game... and The Adventure of Link... and A Link Between Worlds...
Arguably Ganondorf himself. Most of the games he's appeared in before and since have shown him doing some frightening stuff, but Ocarina is his crowning achievement for horror. Planning to slaughter the Gorons, freezing the Zoras, brainwashing Nabooru, etc. And that's not even covering him being responsible for the Goddesses flooding Hyrule in Wind Waker in a last ditch effort to stop him.
The very form of Ganon in this game is truly demonic-looking. In the earlier 2d games, Ganon basically looked like a giant moblin, making him somewhere between a Pig Man and a humanoid bulldog. This incarnation of Ganon is a hulking bipedal abomination with tusks and horns and scales and hooved legs and a draconic tail, all combining into something menacingly monstrous.
Death Mountain's whole 'Raining a volcano on top of you' segment, especially since there's no real build-up to it — one second, you're leisurely climbing up the mountain, the very next, the sky turns blood-red, the ground shakes, and giant rocks are falling on your head (the section is programmed so rocks will always fall on your head no matter what you do). And if you didn't get the hint earlier and buy a flame-resistant Hylian Shield, you're screwed.
On the plus side, it's Nightmare Retardant as well, since it doesn't really attack you; it just stays in place, waiting for you to slaughter it and collect its carapace.
The House of Skulltula in Kakariko Village. Go inside to find yourself in a dark room filled with cobwebs, and then the Skulltulas themselves drop down. They don't hurt you (if you don't hurt them...) but it's revealed that these were a normal family cursed into becoming Skulltulas, with no hope of escape unless some brave Hero of Time found time off his quest to collect Gold Skulltula tokens. Parts of their human faces are easily seen in the Skulltula, all twisted in some form of agony.
The fact that they were actually benevolent and happy to help Link somewhat takes the edge off.
Normal Skulltulas are quite creepy anyway; you see a giant spider, walk towards it and OH MY GOD ITS BODY IS A FACE!
It's daylight, and you're casually sauntering about Kakariko Graveyard, entering the graves in hope of finding heart pieces. As you enter one, you notice a man huddled at the back of the grotto/grave. And then it gets up and SCREAMS, paralyzing you. Congratulations, you've had your first encounter with the Re-Deads.
The Redeads are even worse for newcomers to the series, due to the fact that it may not be clear that they come back to life after being defeated.
As if coming out of the Temple of Time to see what has become of Hyrule wasn't enough, one of the first things you see as an adult in Hyrule Market, a formerly safe place to shop and talk to people, is a horde of Re Deads.
Oddly, the blow is somewhat lessened by the fact that in the Market (and the Market only), their screams don't paralyze Link, making it a trivial matter to slaughter them. Then, it's also easy to see what they do to a nearby Re Dead corpse after you've defeated it. Ever wonder why Re Deads' lifeless corpses stay on screen for so long without disappearing?
You can't see their faces anymore in the 3DS remake. This is because they don't have any heads anymore. It's not the porting team being lazy, either, since you can still see their bodies, just not their heads.
The Bottom of the Well. The boss there is a huge lump of flesh with multiple skinny, pale arms sticking up. Go near the arms and they grab you, then the huge lump of flesh leaps out of the ground and moves towards you slowly, groaning all the way, while you flail about in the arm's grasp. Oh, and the walls and floor look like exposed innards complete with a few skeletons scattered about.
The way to reveal the Dead Hand is to let one of the smaller hands grab you. The slender, blood coated arm that reaches out of the ground like a flower, swaying in perfect synchronization with the others, grabs you and preventing you from moving, while the large hand attacks, making a horrible noise as it does so. The way the monster's neck is out-stretched and looking up resembles a hanged man. The way it wiggles as it comes toward you looks like a hooked fish suffocating to death. Once it reaches you, it lowers its head, and Link is staring into black holes that once held eyeballs. It grins at you as it shivers and takes a bite out of the hero before scurrying away with its head lowered. Need to stay up late tonight?
Also, the fake walls, which are really eerie to pass through, and the fake floors, which can be hard to spot even with the Lens of Truth. If the Water Temple is the designated Scrappy Level, then the Shadow Temple and Kakariko Well are the Nightmare Levels.
On an added note, the room that you fall into through the fake floors has a poisonous pond in the middle. That's fine and all, but look at the "plants". In reality, they're arms and hands, presumably from the victims of Dead Hand.
The Master Quest version of the Bottom of the Well is even more nightmarish than the original. In the original, you can grab the Lens and be out of there in five minutes if you know where to go, because the room that has it is right next to the entrance. In the rearranged MQ edition, you HAVE to brave the entire place, and not only that, deal with constant Wallmasters. This includes a Wallmaster and a Floormaster in the SAME ROOM. Nintendo's official guide to that room just tells you to "RUN."
There is one room of nothing but coffins and Gibdos. You have to open all the coffins, which releases several Keese at once who then immediately catch on fire, and to get the key from the room, you have to jump inside a coffin. You'll quickly learn that Gibdos are Re Deads in disguise. If you are reading this in the dark, good luck sleeping tonight.
In the MQ remake, that room has no key. That means that players who remember that room and go in there expecting to be rewarded for fighting the Gibdos get nothing. Oh, and the first Gibdo is right in front of the door. Good luck reacting to that!
The MQ version of the dungeon also packs in more Redeads; they put a Redead right next to the entrance ladder to catch out those lacking in patience, and the Lens of Truth now appears right in the middle of a large group of Redeads. It's absolutely nerve wracking to try and get that item, hoping the Sun's Song doesn't run out at the worst possible time...
As if the well couldn't get creepy enough, smack in the middle of it there's a large wooden X shape called the Saltire with a pool of blood underneath it. It's pretty easy to assume that people were tied/crucified to this thing. Not creepy enough? Now remember that the floor directly beneath this thing is fake. The implication sets in that after being tortured to within an inch of their lives, they were dropped into this room to die.
Fridge Horror sets in when you realize that the villagers are probably drinking from this water. The bones, blood, and piles of rotting flesh, not to mention the dead hand and the helper hands, are probably leaking into the well.
The people are also blissfully ignorant to the fact there is essentially a torture dungeon underneath their town.
The well is said to be in the same place the man with the eye of truth's house once stood. One has to wonder what went on in his basement back then, and the origins of the dead hand.
In the original, Surprise Skulltulasnote (that is, Skulltulas that hide in hidden cubbyholes in the ceiling—you can't see the hole or its contents, but it's there) don't appear until the Shadow Temple. In Master Quest, they drop one on you in the freakin' Dodongo's Cavern. Dear God.
Pfft! That's nothing. In MQ, try the room in the Spirit Temple beyond the room where the rolling boulders were in the original. In the original it held a small key and a Like-Like. No worries. In Master Quest... TEN BIG SKULLTULASnote (Well, six at first anyway) jump down to scare the ever-loving shit out of you!
It gets worse in the 3DS remake. The ORIGINAL graphics of this game tried (and failed) to show the Shadow Temple in A Form You Are Comfortable With. In the remake, each skull has been replaced by a full skeleton! Those aren't rooms full of skulls, they're actually rooms full of crushed skeletons. Oh, and Dead Hand actually looks like a quivering blob of pale flesh, with the dark spots looking like bruises. Maybe Dead Hand was formed from the flesh of the skeletons that make up his room?
Speaking of, the Dead Hand has hands in every place except where it should. those are bloody stumps. Mhm.
One of the things the skulls say to you if you get close enough is "Shadow Temple... here lies Hyrule's blood-stained history of greed and hatred...", implying that at some point before this game, the Shadow Temple was a very active and grisly dungeon/jail/torture emporium used by the royal family against its enemies, instilling fear upon the whole of the populace. It's a bit like the Black Palace of Lecumberri in a way. So, what does that make Bongo Bongo?
While jumping off of the boat and to a nearby ledge is the right course of action, one of the player's guides still makes it frightening by noting that few things are as they seem in the dungeon, implying that there could be something dangerous or creepy lurking there.
In a room after you get off the boat, it's surrounded by Floormasters. Remember the Saltire in the well? there's another one with a blood-stained floor as well.
In the 3DS remake, the day when you play the Shadow Temple and board the ferry will be the day you gain insomnia. You'll see. There are TONS of ghosts floating about the room the ship is going through.
And then the ship starts falling. Not sinking, FALLING. And if you don't manage to find the nearest expanse of ground and jump onto it within three seconds...
The Forest Temple. From the dark atmosphere, to the enemies (Skulltula, Wallmasters and Floormasters, Stalfos, the four Poe sisters), to the boss (Phantom Ganon), it's a generally unsettling place. However, most creepy of all is the music.
And around one minute and ten seconds into the track, demented laughter starts playing in the background.
When you first enter the boss room, it appears to be empty. If you try to go back, spikes pop up to box you in the empty arena. Then, surprise! Ganondorf on his horse, coming right at you!
Phantom Ganon, who then proceeds to rip his own face off!
Paranoia is rampant in the Forest Temple. A lot of veteran players just note "something about it" that specifically makes them want to turn around and make sure nothing is behind them.
Look at those pictures in the boss room just before you fight him. Few players note it, but Link is in all of them. Every single one of them. Just sitting on a tree, like it's his business. Creepy.
It doesn't help that even after you save the members of the House of Skulltula, their faces look like the Happy Mask Salesman's. (see below)
Wallmasters and Floormasters. At least Navi gives you a warning about the Wallmasters, but the Floormasters would split into three little bitty Floormasters. If you didn't kill all three fast enough? They would turn back into the one big Floormaster. Oh and hey... let's not even mention the Invisible Floormasters...
There are even points in the Spirit Temple (especially Master Quest) where hitting a wrong Sun Switch will release one of those things.
There's a room in the Spirit Dungeon of Ganon's Castle where you have 4 Sun Switches. The wrong ones ALL release Wallmasters. Oh how lovely it is to hear the "incorrect" sound effect followed by that horrible rushing wind...
It's even creepier with that ominous sound effect that plays whenever one of them is hovering over you, closing in...
The game designers were cruel enough to place multiple Wallmasters and Floormasters in the Spirit Temple and Bottom of the Well in the Master Quest version of the game, including ones that come out of nowhere if you push a wrong sun block into the sunlight. The sun blocks in question are often the ones closest to the light, which you'll probably push into the light first, on instinct.
Beta versions of the game had the Wallmasters look like THIS◊. Imagine turning a corner and running into that monstrosity.
The Invisible Skulltula Cavern past Zora's Domain as Adult Link, where Jabu Jabu used to be. You gain access to a hidden cave passage, and enter to find nothing... until you're slapped in the face with invisible monsters.
Get either a cartridge and a Gameshark, or an emulator and ROM, and use the codes that allow access to the leftover prototype areas that are still in the game code (for best results use emulator + Master Quest debug ROM which contains most of the unused rooms). Some of these are absolutely creepy, either due to their unfinished nature, odd bugs, or the lack of music.
So, after pulling out the Master Sword, Link gets put into a seven-year coma... But while his body has matured, he's still basically a ten-year old. A ten-year old who, first thing after leaving the Temple of Time, finds the Town Market in ruins and filled with zombies. Not to mention he has to go through all those temples with equally scary things, like those Wallmasters and other zombies and freaking Dead Hand. And he experiences all this while he is pretty much still a ten-year old boy. Imagine going through a well full of rotting corpses and dead things while you're 10.
The worst part? Link is actually in his 10-year-old body when he goes through the Well, after having just gone through three temples in his 17-year-old body. So he's not only got the mind of a ten-year-old, but the smaller body and diminished strength of one, too.
The Anubis monsters and the way they hovered ominously above the ground in the Spirit Temple...gaah. They just stare. Nothing else.
Gohma's first impression on the player, being not only the first boss, but a giant parasitic insect.
Speaking of early bosses which are terrifying, King Dodongo. He's not terrifying in his own right, he's actually pretty funny looking. However, the trick to beating him is to throw bombs down his throat. And his death scene is even worse. He rolls into a pit of lava, and you get to watch him writhe in pain for 15 seconds while his skin gets progressively more and more charred. Eventually his own body absorbs enough of the heat that the pit of lava solidifies, leaving his head and front legs sticking out of a patch of rock.
Another thought: the only way to enter his room was to fall down a hole. There was no exit. How long had he been there, trapped in a small circular room with a slightly smaller pit of lava in the middle? Just him and the lava. Alone. Really, Link's murdering was a more of a Mercy Kill. Still horrific.
That one Redead by the door as you escape Ganon's Castle. Dear God, the game designers were cruel by placing that enemy there, especially as it's the sole one in the game which isn't stunned with the Sun's Song (except in the 3DS remake), and is placed just right so careless people will have to run straight past it.
Lake Hylia when the water is drained is creepy. It looks like a giant crater with a little bit of water and a large mound in the middle. It's made even creepier by the fact that as you head towards the center, the overworld music stops playing and it starts storming. Not to mention Lake Hylia is now swarming with Guays and more Blue Tektites than ever before, something that doesn't change even after you complete the Water Temple and refill the lake to its former glory.
It's actually even worse after you refill it, as well as Zora Fountain in the future. You're just swimming along leisurely, and then you get a face full of Octorok out of nowhere! These guys appear out of nowhere, like little aquatic Skulltulas.
Lon Lon Ranch at night as young Link has a similar problem: Guays everywhere! The sounds of Gold Skulltulas only add to the creepiness.
Don't mess with the chickens! They hunt in packs and never quit until you're dead!
Jabu Jabu's Belly. You start by feeding Jabu Jabu a fish so he swallows you. And that's just the start. Hitting the walls (read: his insides) doesn't cause the usual sword rebounding effect, but instead your sword completes its animation as you hear a groan and see a little splatter of blue "blood". There are strange holes in the "ground" that take you to unexpected destinations. At one point you have to sever a couple "Parasitic Tentacles" to advance. Some areas have water... or what we can only hope is water given where we're in. And to top it all off, in the Master Quest, there are cows in the walls. Cows that serve as shootable switches.
Turning around as soon as you get in shows his huge mouth, which is closed and full of sharp teeth.
Admittedly, the thought of cows inside a big fish is a little funny as you think about how they got there... then you see a live cow at the bottom of a pool of stomach acid/water, probably taking forever to die.
And it is so much worse in the 3DS version. High-quality graphics show realistic yellow-pink blotchy walls, sphincters for doors, and connective tissue in the hallways. Not to mention the disgusting way Barinade dies.
The beta version of the game seems like it was probably worse here, since guess what feature the fan sequel/remake of Ura Zelda brings back? Invisible Redeads. Yes, Redeads only viewable through the Lens of Truth. Good job the released game never had that in the Shadow Temple...
Big Skulltulas. In glorious 3D. They were bad enough in the original, but when that's combined with Art Evolution and 3D, it makes them downright horrifying.
The Stalchildren, creepy skeletons of children that spawn nonstop at night when you're Child Link. Destroy enough of them and a giant one appears!
Worse, crossing Hyrule Field to get from Kokiri Forest to Hyrule Castle takes all day, and unless you roll nonstop, the bridge will retract just before you get to it, leaving you to fend off Stalchildren all night (eventually spawning the aforementioned giant Stalchild) or flee to Gerudo Valley or Zora's River* Going to Kakariko Village or Lon Lon Ranch doesn't work because time doesn't pass at either of those locations for safety until the sun comes back.
This is the first time we see Like-Likes as three-dimensional creatures. The way they move and are textured, coupled with their property of eating special tunics and shields, makes them so creepy to fight.
Ironically, the "puzzle solved" sound. It's loud and can make players jump because it sounds out-of-place in a game that otherwise uses more modern video game sounds. It's particularly startling in dungeons, as it runs counter to the eerie calmness of the background sounds and music when there are no enemies around.
Volvagia's death: It flies around the Boss room, writhing in pain and ultimately burns off its own flesh, revealing its skeleton. Creepy! The battle itself isn't a picnic either, considering that Volvagia routinely attempts to bring the roof of the Fire Temple down on your head, something not seen in any other boss battle up to this point.
The Great Deku Tree's death, in which it withers. Unfortunately toned-down in the 3DS remake.
The resulting loss of protection shows seven years later: When you come back to Kokiri Forest as an adult but before completing the Forest Temple, it's filled with monsters! No wonder all the Kokiri are huddling in their homes scared out of their minds. Fortunately it gets better after you clear the Forest Temple and the Deku Tree Sprout emerges to purify the forest once again.
The Bubble enemies are enormous when you're playing as Kid Link.