The end of FC's Chapter 1 has Don Capua, who's the first indication that this game isn't as saccharine as it seems. While Josette and Kyle Capua, his underlings and younger siblings, were almost Jessie and James levels of goofy, non-threatening criminals, you first meet Don when you walk in on him planning to kill all the hostages from an airliner because they know too much, and he proceeds to go Ax-Crazy on your party, complete with a disturbing gritted-teeth portrait and hunting metaphors. This is the first time in the game a villain has threatened you with death, a stark contrast to the lightheartedness of everything before. Possibly making this worse is that he's Brainwashed and Crazy, and genuinely doesn't remember any of this after you beat it out of him. Imagine if he had killed someone, only to wake up and not remember doing it.
The Dissonant Serenity as Joshua describes a child committing horrible acts of murder day after day, treating the whole thing like a child's fairy tale.
FC's laid-back pacing and cheerful tone work wonders to make the threats introduced in SC feel that much more realistic. After two games of rich world-building, the thought of Weissmann succeeding in his plan to have all of Liberl mind-controlled is depressing to say the least.
Most of the Enforcers are varying degrees of creepy, but Walter the Direwolf deserves a special mention.
Tita: Wait...B-B-But...If the buildings collapsed, all the people inside would get hurt!
Walter: Heh. You catch on quick, little girlie. Some of 'em would get crushed under the rubble, their arms and legs mashed into jelly, left screamin' like pigs...Others? They'd get quick deaths. Heads shattered like eggs, spillin' their brains out on the road for everyone to see. Heeey, I've got an idea! How about we do that to you instead? That blond head of yours looks pretty fragile to me.
While Bleublanc is normally too hammy to be scary, he can be pretty terrifying when he wants to be, and some of his actions have disturbing implications, such as his I Have You Now, My Pretty attitude towards Kloe. The report on him in one of The Third's Star Doors also contains some creepy elements, such as noting that one of the "unappreciated treasures" he once stole was the Trophy Wife of a famous general. While it initially seemed like he had good intentions, rescuing her from an abusive marriage, the report then notes that she was never seen or heard from again.
Renne's truecolors. Much like Albedo, her insanity is chillingly realistic, as almost all of her dialogue post-reveal and pre-HeelFace Turn is deranged babbling rather than simply stating her love of carnage and death.
Renne's past before joining Ouroboros didn't help. It was so bad Falcom had to censor it from every release after the original release. Had XSeed not decided on localizing the PC version (they thankfully only localize the PC version), the truth would be left unknown to the western fanbase.brief explanation(spoiler!) She was forced to be a prostitute while also becoming subject of the human experimentation of a cult later revealed in The Legend of Heroes: Zero no Kiseki. The experience was so agonizing for her, she had to create imaginary characters and physically cut her own skin to cope with it.
The doll replicas of Joshua look mildly unsettling, but having to fight them is strongly implied to be outright traumatic for Estelle, who has a nightmare about it afterwards.
The Aureole is a weirdly grave part of what has been, on the whole, a pretty classic JRPG. A treasure from the Goddess that goes on to more or less break mankind's will by giving them unlimited wishes, to the point of trying to kill off a rebel effort to free humans to live and make friends again, all out of what appears to be good intentions is juicy and oddly terrifying in a low key, background info sort of way. The number it does on Weissmann doesn't really make things much better.
The most terrifying thing about this comes from the fact that lots of ancients at the time had grown dependent on Aureole. Breaking the will of the people back then resulted in them not knowing how to survive on their own, so much so that 90% of the remaining population in what ended up becoming Liberl died. Having to survive without such advanced technology must have been chaos back then.
How did this societal degradation even start? The inhabitants used the Aureole to essentially grant them everything they ever wanted with it's power over Space, essentially mentally turning the Liber Ark into a giant farm due to the eventual overuse. Imagine the state of the humans in WALLE, replace the robots and flying couches with an omnipotent genie that serves everyone and you can pretty much imagine what humans were like back then.
It bears noting that a man who orchestrated a massacre of an entire village just to prove how sinful man was then turned one of the survivors into a Tyke Bomb did a Fusion Dance with a Lotus-Eater Machine. Imagine what would have happened to not only Liberl but Zemuria as a whole had he not been stopped.
The Hamel incident. An entire village was destroyed in a horrifyingly realistic depiction of Rape, Pillage, and Burn, with the "rape" part not being an exaggeration. Joshua's description of what happened to him as he was fleeing is the worst part. Harmful to Minors doesn't even begin to cover it. (As Joshua fled with his sister, they ran into a soldier, who attempted to sexually assault her. Without thinking, Joshua grabbed the soldier's gun and shot him in the throat. And the soldier didn't even die instantly, he spent a few minutes sputtering and bleeding out, which the text lovingly describes. Joshua was just a child at the time, and these events rendered him nearly catatonic... which allowed Weissmann to mold his personality as he saw fit.) It's telling that this incident serves as the Start of Darkness for multiple characters across the whole Kiseki Series.
Weissmann's S-Craft, Another Dimension. It looks more like something from a horror game than a JRPG: it has the party falling into a blood-red sea of faces, grabbed by bloody hands, then impaled on bloody spears.
The brief glimpse of Kevin's true personality at the end of SC. Especially given how he acted like a lovable jokester the rest of the game, and unlike Olivier gave very few hints he was Obfuscating Stupidity. His face portrait changes make it worse. The only thing that mitigates it is his target totally had it coming.
The Salt Pale incident, which is revealed to the player in the 3rd. Basically, a giant tower of salt appeared out of nowhere in the state of North Ambria, turning HALF of the country into a sea of salt. If that's not terrifying enough, the text implies the damn thing would, eventually, cover all of Zemuria if it weren't for the fact that there is a giant river between it and the rest of the continent.
The moment when Kevin's backstory is fully revealed. Firstly, his own mother went insane and tried to commit murder-suicide with him. This is easily one of the greatest moments of Adult Fear in the series. Nothing fantastical involved here, no Demonic Possession, just a normal human pushed to the edge. We even see a still image of her, faceless, with a Slasher Smile, moving in to strangle Kevin. After that we find out what really happened with Rufina. When Kevin's orphanage was attacked by Jaegers, one of them kidnapped Ries and Kevin chased them to a sealed room housing an Artifact of Doom. The Jaeger touched it and transformed into a horrible monster, but Kevin's Stigma triggered and absorbed the artifact's power, shooting out a barrage of spears. We don't see it, but according to Kevin's narration, what little was left was barely recognizable, just chunks of flesh splattered across the room, and Kevin was still in a state of uncontrollable bloodlust and was poised to attack Ries, so Rufina sacrificed herself. We get another artwork, this time of Rufina impaled on several spears, blood smeared across the floor. No wonder Kevin is so messed up after all that. You will never see Kevin's second S-Craft the same way again.
The Gehenna section of The 3rd is fairly disturbing. Kevin has to face several demonic versions of the people he killed, such as a corrupt clergyman who caused his Start of Darkness and a boy he had to Mercy Kill. The last miniboss is his mother turned into a ghost, since he feels guilty over her death even though he didn't kill her.
Star Door 15, "Paradise". Being Renne's backstory before joining Ouroboros, it's a terrifying moment filled with copious amounts of Adult Fear. Simply put, Renne was part of a luxurious child prostitution ring, used by rich, higher-class people. This is already awful on its own, but what makes that scene so scary is Renne's point of view: At first, she seems to talk with a few fellow children at Paradise. She's apparently not doing any, ahem, "work" while the other kids are giving her tips about ways to satisfy their customers: "Always seem like you're happy while doing it" "Think about what the customer wants and how to make it feel good", and the like. However, little by little, the children mysteriously disappear: It goes on until there's only one left, who lashes out on Renne, screaming that it's all her fault and that she deserves it. Finally, he disappears as well, leaving Renne as the only child left. As she's about to get to work, it's revealed that all the other children seen by Renne were actually delusions of her own mind that she used to deny the reality of the situation and keep her mentally sane. The worst part is, that's actually a common symptom with victims of abuse. Either that, considering how Gnosis worked, there were indeed other children but Renne subconsciously absorbed their personalities when it's her turn to "work", which isn't much better. When Loewe and Joshua burn down Paradise, they find Renne, naked and her body full of scars, and decide to save her. "Paradise" is such a shocking moment in the Kiseki franchise that not only has it been heavily censored on the PSP and Vita versions, but "Paradise" has become an Unusual Euphemism in the fandom for horribly bleak and dark moments.