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Nightmare Fuel: Metal Gear Solid 2: Sons of Liberty
The corpse in the locker near the Engine Room in the Tanker Chapter.
That entire sequence inside Arsenal Gear: The Colonel and Rose are both revealed to be AIs. The AI gets corrupted by a virus, and the Colonel starts spouting nonsense. Some of the codec calls you receive in this section is truly horrifying: You're naked and unarmed, and while there's definitely something wrong with what's going on (besides you being naked, of course), there's nothing certain except that you really should get moving to finding your suit. Then you get a CODEC call from the Colonel. "Raiden. Turn the game console off RIGHT NOW." This line is especially jarring if you have been playing the game for an extended period of time. From this point on, the CODEC calls are filled with terrifying Word Salad Horror, a lot of which is aimed directly at the player.
Adding to that, for some of the calls, the Colonel's portrait is replaced (at random) with an X-ray image of his face. This image◊, which only ever shows up for a split second, with no warning, is truly one of the most horrifying shocks in the entire series, and would make a great page image, were it not such a huge spoiler. To match that, occasionally Rose's AI will be pictured with glowing white eyes.
Due to the randomised factor mentioned above, each time playing through this section will be unique, which only adds to the horror. In the video above, the line "Snake, you're all alone and surrounded by bad guys" is especially creepy.
The line "Kawanishi-Noseguchi, Kinunobebashi, Takiyama, Uguisunomori, Tsuzumigataki, Tada, Hirano, Ichinotorii, Uneno, Yamashita, Sasabe, Kofudai, Tokiwadai, Myokenguchi." The creepy thing about these seemingly random words is that they keep showing up throughout the series. After MGS2, The Mammal Pod in Peace Walker also spouts them off when it's drive uplinks are removed, and Sunny uses them as lyrics in a tune while making her eggs. A decade later, Raiden asks Bladewolf what it means, and even it has no idea. note It is apparently a list of stations along an electric rail line in Honshū, Japan.
Codec calls with the Colonel in the beginning of the game. Then the Colonel tells Raiden that they removed all his blood and replaced it all with artificial blood that includes nanomachines.
The names of the parts of Arsenal Raiden's entering or exiting. (The 'oh WHAT' locations the AI throws at you are a relief, which, yeah.) Jejunum, Ilium, Ascending Colon - it's snicker-inducing at first, but then you stop to consider it, and you realize these are all parts of the human digestive system, so basically Arsenal ate you alive.
The strange empty vortex where you fight the Metal Gear Rays (The Rectum). Nothing but a triangular platform hovering over what appear to be clouds surrounded by darkness. As you fight, an endless wave of Rays slowly walks up to the platform and... wait. Waiting for their turn to fight you. The worst part- there is no apparent way to enter or exit this room (Raiden climbed a ladder to get there).
That "room" must have been designed to be as unsettling as possible. Was it just a holographic simulation created by a horrifically damaged AI? But in the next scene you're obviously outside and on top of Aresnal Gear
They were more set pieces, and a puzzle than anything you had to actually, seriously deal with - but all those fucking cockroaches in the Big Shell.
Arsenal Gear itself. Imagine a huge black beast loaded with nukes and Rays resting just below the water's surface. Then think of all the people who were utterly crushed when it crashed into NYC.
Those are sea lice, actually. And in a codec conversation, their presence on the Big Shell is explained. Emma is appropriately terrified of them.
The part of the game where you have to protect Emma Emmerich from on top of a platform is both hectic and a bit jarring in itself... She's being hounded and hunted relentlessly by Vamp throughout the whole ordeal and fight. There's a bit of Adult Fear thrown into good measure along with the horrific inevitable out come which falls into the deep lines of some serious tear jerking territory.