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Nightmare Fuel: XenoSaga
Ah, ma belle pÍche, there's no need to tremble like that...
Despite being a Teen rated game, Xenosaga sometimes has scenes that are so frightening and disturbing that it should very well warrant a mature rating.
The first episode of the series features a scene in which the main antagonist Albedo (who is truly one of the most insane and horrifying villains in video games) after murdering a whole score of little (humanoid robot) girls and scattering them across his room, traumatizes a little (humanoid robot) girl by sawing off his own arm and head in front of her. And then mind-raping her... leaving her a mindless doll, apparently. To make this worse? In the Japanese release, he cuts his head off. In the US release, this is censored.... To ripping it off with no assistance. Also, note that, after ripping off his head and speaking through it, he stomps on it. Ew.
The Creepy Child version of Albedo is equally this, especiallly during the end of Episode II.
One of the most frightening things about Albedo is how convincingly insane he is. Most "crazy" villains are just exceedingly vicious sociopaths; Albedo's constant stream of half-coherent babble, biblical allusions, and bizarre figures of speech goes a long way towards making him seem not just violent and cruel, but completely batshit crazy.
Albedo: There's enough of it, we can afford to waste as much as we want! Like my head, you see? HAHAHAHAHAHAHA!!!
Albedo's theme from the first game. It's creepy enough as it is, but mixed in with the Mind Rape scenes with MOMO, and it becomes flat out terrifying.
In the first episode of Xenosaga, there is an unpleasant scene where we get to see the effects of a gnosis' touch upon humans. Despite the otherwise hammy acting in much of the game, watching the poor soldier who gets grabbed by a gnosis struggle and thrash, go limp, turn to salt and shatter is deeply disturbing.
There's that one scene, thankfully only shown in a couple half-second flashes, of Febrona's corpse being eaten by a horde of mutants (One of which you later meet as a That OneBonus Boss). Nothing is shown, just the mutants in a big huddle, the horrible, horrible chewing sounds, and Febrona's head jerking randomly as they tear at her body...
There's the creepy looking 27 Series Asura Realians, who weren't even nearly ready for combat, but were released during the Militian Conflict. What happened? They, along with the normal Realians went rogue. A few went and killed Shion's parents right in front of her eyes when she was about eight years old. This leads to a touching scene where kid Shion was kneeling on the ground, her mother's blood pooling in her hands, with her chanting that she "has to put it back". They sadly censored this, however, when they removed every instance of blood in the game. What was once a Tear Jerker became more of a Creepy Child moment, until you could understand what was going on. It was also in that moment Shion in her sorrow summons the Gnosis to that planet and the rest is history.
Gnosification tends to be rather nightmareish.
The beginning of Episode 1 really sets up how horrific gnosis can be as they massacre the crew of the ship you just spent 2 or 3 hours walking around. Until KOS-MOS' CMOA, no one even manages to touch them, while the AGWS units and cannons outside of the ship are dwindled down to nothing, and internally the foot-soldiers and realians are crushed, turned to crystal and shattered, and thrown about in a bloody mess, with only AGWS units being able to stand against them and even then just barely as the AGWS can possess some of AGWS units.
In Episode III there's a brief glimpse of Kevin's mom gnosified as he escapes the planet.
Episode I also has the gnosified humans stored within the Durandal
The concept of the U-Do, itself: An alien being (he's actually God, sent into the Heroes' realm as a child and later, a flying Ark) that spies on the whole of humanity, even though he does it for scientific reasons more than anything.
At the end of Episode III, chaos' consciousness resides within the dilapidated remains of Kos-Mos and is floating in space; considering that he has lived at least 7000 years already, he doesn't seem to mind that much.