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Nightmare Fuel: Ib
One of the first puzzles involves heading into a hallway with a bunch of people with colored shirts in frames. There are six, and the trick is to find out who's telling the truth. Once you do that and find what you're looking for, you hear something from the hallway (by this point, you'd have entered a room with a statue and tiles). Once you get out, all of the picture frames have red splattered all around them, and the truth-teller is completely gone from its frame. In a show of irony, they all yell "Liar!" It's really unnerving.
Mary, the psychotic painted girl who wants to become real.
There's an optional sequence you can encounter by switching back to Ib immediately after the The Reveal... or barring that, completing the doll room event successfully. It's a three part sequence, regarding Mary going off the deep end. First she runs out of the room to stab a mannequin head, which bleeds. Second, her sprite will visibly begin to follow Ib from behind — something that NEVER occurs anywhere else in the game, even in cut-scenes. Third, she'll wander around endlessly, ignoring the player completely. Couple this with some unnerving Madness Mantras and vaguely threatening dialogues and you've got the player completely freaked out.
The dolls. THE. FREAKING. DOLLS.
The simple fact that until near the end of the game, Ib can't see the dolls at all. Her mind replaces them with completely harmless bunnies, so she can't even see why Garry would find them upsetting.
The doll that stalks Garry down a hallway. Her tendency to use Offscreen Teleportation to get around is more than a little upsetting. Also if you kick her her head keeps following you.
The Giant Doll. It first appears in the alleged bunny room, and continues to appear ominously in several of Garry's solo sequences under certain circumstances, peeking over the top of walls and pillars and looking back and forth. Sometimes when it does that, it will then look straight at the screen and giggle.Then in the second doll room, the Giant Doll starts crawling out of a painting. If it catches Garry before he can escape the room, he is later found by Ib and Mary, having suffered a mindwipe. In a normal playthrough Ib's able to help him, but if you really screwed up before that point, Ib can't save Garry and you end up with one or the other of the worst endings in the game.
Even succeeding in the second doll room gets creepy; while Garry manages to escape the room, the thought that the dolls are still there is more than unsettling. Also the split second before Garry escapes the room, the dolls suddenly all turn their heads at once. They don't look at Garry, they look at the player.The Fourth Wall Will Not Protect You strikes again.
In the regular art gallery, a dialogue choice with another art gallery patron reveals that 9-year-old Ib thought the headless mannequin statues were scary before they started attacking her in the phantom gallery.
Those roses. When you take damage, it wilts. Fair enough, since it's this game's version of a Life Meter. Except it works the other way around too; Garry mentions that before he met Ib, whenever his rose took damage he'd notice physical wounds opening up on his skin. Imagine if you'd left your flower behind, never realizing its significance. You could just be walking down a hallway when a huge cut opens up on your arm, and since you don't have a vase it might never heal...
In Version 1.04, if you have Garry kick the mannequin head and see the "Hanged Garry" message, then in optional dialogue later on he asks Ib if there's something around his neck...
The Sketchbook World is already quite disturbing. Even more disturbing that Mary is actively looking for Ib and Garry, and at one point very nearly finds them. Even more disturbing after you open Pandora's Box and every once in a while sharp pointy objects randomly fly out at you. And then Mary does find you...
The "Welcome to the World of Guertena" ending. Garry loses his mind in the doll room, Ib is unable to bring him back to his senses, Ib has a breakdown over this, and Mary has grown so fond of Ib that she can't bear to go to the human world because it would mean parting with her. So she instead keeps Garry and Ib in her world. Forever. Not to mention she has a freaky Slasher Smile in the final scene.
The ending A Painting's Demise is very disturbing. With Garry driven insane by the Doll Room and Ib too distraught to leave, Mary abandons them and leaves the Fabricated World. Only, as she steps into the "Alternate Gallery", the writing on the walls threatens and warns her not to leave. When she does step out into the "Real Gallery", there's no-one around and the Gallery's door out is locked. As Mary gets frightened and tries to find another way out, it slowly gets darker, and dark paint drips from the ceiling like blood. Other nice details include the "Embodiment of Spirit" rose sculpture fading into a withered and grey husk with a warning about Mary's "fabricated heart", the poster advertising Guertena's Art Exhibition at the entrance turning into an image of a face-down (dead?) Mary◊, the windows overflowing with a creepy bloodlike red liquid, the creepy crooked writing saying things like "B Y E B Y E M A R Y◊", the painting of "Abyss of the Deep" bleeding out into the Gallery, "A Well-Meaning Hell" turns into Tones of the Dark Gallery◊, and then if you repeatedly examine Mary's inventory screen as things get darker...
The Bonus Dungeon. There's such charming things like discovering Garry's lighter is out of oil right when you're in a pitch-black room, a giant sleeping snake that you have to get past, giant flowers that grab Ib's ankles and eat her if she tries to walk by them, a painting named "Mistake" escaping its frame and wandering around, a vase that has blood in it for no apparent reason...
When Ib and Garry are captured in the Sketchbook world. One moment they're staring into a toy box, the next moment they've been shoved into it and find themselves trapped in an area filled with statues... and dolls... and mannequins... and more dolls... and more mannequins. To make things ever better, Ib's rose is missing. Depending on what story path you're on, either one of the dolls steals Ib's rose and gives it to Mary, and Garry ends up having to trade his rose to save Ib's life, or Ib finds her rose and discovers that the impact from the fall knocked all the petals off except one. And there's no vases in the toy box so no chance for Ib to recover her rose. Either way, you're in bad shape in this section.
The painting "Malice's True Form". You encounter it in a dark room, it makes sounds and moves slightly when you look at it closely, when you move away from it you hear something fall to the ground and it makes the weird noise again, then you go back to find that there's nothing in the frame that had held it. And then later you are in the area with the giant snake and find that "Malice's True Form" is right there in the hallway. Eek.
Carrie Careless and the Galette des Rois. A charming little storybook, drawn in crayon, about a little girl celebrating her birthday. There is a coin in one of the cake slices and she accidentally swallows it. But that's okay, because it was a lucky coin, so now she'll have good luck. It turns out to be the key to the study. The mother of one of the girl's friends can't find the key now. The friend, realizing that it was the key and not the coin that the girl had swallowed, decides the best way to get the key back is to kill her. The end. It's also scary in a meta way, as some people have had it crash their game.
It turns out to be perfectly okay, he really did need a rest and he woke back up just fine, but the part in the Bonus Dungeon where Garry takes a nap is quite disturbing, especially when he says it feels like his legs are becoming one with the floor, or the "....." if you try to talk to him after that.
Even scarier is the sequence you have to go through before going to the secret room. Garry falls asleep, you can't go outside alone, and you've done possibly everything in that room until there's nothing to do until Gary wakes up. Of course, when you check on him, he's not waking up at all, and all of a sudden the next thing you know, the room and everything in it begins shaking about. Check on Gary during this and your dialogue choices are "Garry!" and "Wake up!", and choosing either will just prove to be futile no matter how many times Ib tries to wake Garry up in her state of panic. And since she can go through the Bonus Dungeon alone, imagine her freaking out during this with no one around to give her a sense of security.
Any of the "Ib All Alone" endings, but particularly the one you can get in the Bonus Dungeon, if you sleep too long on the artwork "Final Stage".
"Final Stage". It's a strange, diamond-shaped bed that Ib can sleep on, and she dreams about her birthday. Awful cute, right? Sleep on it too long though, and Ib sleeps forever. "Ib All Alone". Notably, while Ib gets a "nostalgic feeling" from it, if Garry's with her at the time, he won't let her near it because he gets "a bad feeling" about it, and he's right.
Not sleeping on it for too long can be almost as bad. If you wake up in time, you'll find that some of the petals of Ib's rose have fallen off. It really gives the player a sense of wow, that was a close call, and it removes any possible ambiguity to Ib's fate if she doesn't wake up in time...
The fake Garry, who appears if you're on the path for "Forgotten Portrait". When you get to the portal back to the real world, this guy appears, telling Ib there's another exit and trying to tempt her away from the portal painting. If you go along with him, you get "END: Ib All Alone", and if you refuse him and jump through the portal anyway, he suddenly lunges forward as if trying to grab you.
The Reveal that Mary is a painting is disturbing in and of itself, but one of the things that makes it so frightening is that Garry learns about this while he is separated from the girls, meaning if Mary were to attack Ib right now, there would be nothing Garry could do about it.
The mirror. If Garry kicked the mannequin head, checking the mirror after the Separation room will lead to some pretty scary images. Garry's own head may be blotted out (which only Ib can see), both Ib's and Garry's eyes will be scratched out with the word "EYE" scrawled all over the mirror, "NOFIRE" may be repeated to cover the mirror, and the word "Play?" may appear, written in crayon. Creeeepy.
In the Grey Room with all of the Painted Ladies, if Garry kicked the mannequin head, the Hanged Man portrait can have a (random) case of Red Eyes, Take Warning.