All spoilers are unmarked, proceed with caution.
- Pyra's brutal Mind Rape by Malos to restore his Aegis powers has players saying it's hard to watch in the unsettling way, and for good reason. Skye Bennett's performance only adds to the unsettling aspect of it.
Gramps: Rex, are you okay?[Beat], Rex heaves for a momentGramps: Rex?Rex: I'm...I'm fine...Gramps: Could it be...Pyra is in trouble?Rex: I don't know...but, we have to hurry. I have a bad feeling about this...
- The scene opens with Pyra, restrained by the artifical blades, screaming and trembling in agony. To further drive in how much pain she's in, there's also sickly looking ether lines all over her body caused by Malos. Not a pretty sight from the get-go. It's also enough for Rex to stall in pain for a moment, only this time in more pain than before.
Malos: Why are you running? Why are you protecting this garbage? We Aegises don't need these things! You want to be free of them as I do!Pyra: Stop it! I'm not like you at all!
- Next, there's a brief Battle in the Center of the Mind, except it's framed much more like a Hopeless Boss Fight thanks to the ominous visuals. We see a terrified, defenseless Pyra attempting to run away from Malos as he does an Unflinching Walk along a dark fog covering all of Pyra's memories.
Pyra: Stop! Stop stealing my memories!
- After a brief exchange between the two, Malos is suddenly in front of Pyra, almost like something out of a horror film. Malos takes this time to finish the job, but not before Pyra pleads him to stop, still sounding just as terrified as a moment ago.
- This ends up temporarily turning Pyra into an empty shell by the time Rex comes to save her. However, Earlier on in a scene with Patroka and Akhos, it's implied that Malos didn't even need to steal Pyra's memories to restore his Aegis powers, which only adds to how Malos is depicted much more monstrously in this scene.
- The Land of Morytha, a post-apocalyptic modern city full of nightmarish, humanoid monsters known as Guldos, and they are the only organic monsters present in the land aside from Parisax in the Titan carcasses. It is later revealed that these feral abominations used to be the original humans of Earth, who tried to make themselves immortal through overuse of Core Crystals (which were intended to replace dying brain cells). They succeeded and survived the creation of Alrest, but they've mutated so drastically, the only thing human about them is their shape, and some such as the Infernal Guldo, don't even look close to human anymore. These creatures and the ruins of Morytha are all a result of human folly.
- At the start of Chapter 9, we get a silent sequence filled with the haunting choirs of "Past From Far Distance" of a young Amalthus helping those in need. However, thing gets turned into the nightmarish when Amalthus, during a walk in the forest, hears the screams of a baby in a house nearby. The house is being pillaged by someone we don't see the face off yet, as we see him with an already dead mother in the floor brandishing a knife in an attempt to kill the baby. But then Amalthus holds his arm and we see the face of the murderer, it's one of the people Amalthus healed previously. Enraged, he gives him the coldest Death Glare he can give, and during the sequence, we hear the baby cry louder, and louder, until it stops when we hear the scream of the man presumably being killed by Amalthus. The final sequence is a sad Amalthus, holding the baby in his hands, finally saying:Amalthus: Oh Architect, is this the world that you intended?
- Amalthus' true nature. For most of the game, he comes off as a fair-minded, if slightly cold and ruthless leader. But at the game's climax, its revealed that he was so broken by watching mankind succumb to its worst and darkest impulses of years that he's become a bitter, deranged Omnicidal Maniac, convinced that condemning Alrest to oblivion would not just be a mercy, but also the will of the Architect.
- The scene where his true colors are revealed. After dispatching a group of suddenly hostile Indolines, Amalthus appears and, in a tone angrier than he's ever been before, demands that Rex use the Aegis to open the way to Elysium. When Rex questions this, Amalthus loses it, his eyes glowing red as he madly declares to entering Elysium and receiving the Architect's blessing is his right, not Rex's.
- Amalthus's One-Winged Angel form, created from absorbing multiple Blade crystals. After Klaus tells the party how the Guldos in Morytha came to be, it's apparent that Amalthus essentially became a Guldo, but has retained his sapience and some semblance of his original self.
- In a flashback, Amalthus and Zeke discuss about some bandits who Zeke thinks tried to kill him in order to steal Pandoria as a Core Crystal, and explains how due to Pandoria looking quite human for a Blade, that she could be sold as a core with pictures of how they look awakened. Essentially, he's describing how they are putting blades as possible sex slaves. Due to this very dark fact, Amalthus mentions how horrible humanity can be, saying that "as soon as people are denied of something, they try to take it by force".
- Klaus' test of Rex in Chapter 10 is notorious for the sudden tone shift, going straight into Psychological Horror territory and also doubling as a tear jerker. It's just as, if not more nightmarish than Malos stealing Pyra's memories. Despite the English dub's inconsistent voice direction, Al Weaver deserves mention for delivering a chilling performance, managing to capture Rex's confusion and terror throughout all of it.
- Even after it's revealed afterwards that everyone except Pyra and Mythra were manifestations of Rex's worst fears, there's still some added Fridge Horror. The others, including their blades, had very similar visions, which are not seen.
- Klaus' fate. Half of his body is trapped in another universe, while he remains in his home dimension. Physically, only half of his body is visible, with dimensional rift covering the other half. Not only that, but his other half doesn't just refer to his body, but also toward his evil split personality, whom he sees and hears through, and knows every thought of. Oh, and Klaus himself is also unable to die as long as his other half is still alive.