- The very first mission actually involves the titular Nice Guy Zack slaughtering the final resistance force of Wutai against the malevolent Mega-Corp of the Shinra Electric Power Company, securing their dominance over the Planet and unintentionally sparking Yuffie Kisaragi's Break the Cutie moments due to Shinra turning her home into a neutered tourist trap soon after. All of this is played with a disturbingly cheerful tone despite being a case of The Bad Guy Wins.
- Poor Zack's dilemma throughout the game is a nonstop Trauma Conga Line. He has to watch all of his superiors and role models turn into horrible and insane murderous monstrosities, has to fight every single one and watch all of his former mentors die in disgrace, gets tailed and attacked by the very group he swore loyalty, struggles to come to terms with whether he'll turn into a monster too, and eventually gets mowed down by gunfire in an empty field for defending a comatose friend and wanting to see his new girlfriend. All this pain because he wanted to be a hero.
- Cloud's comatose condition is as sad as it is creepy. He's more like a lifeless doll than a human at this point and Zack talking to him to get some form of comfort shows the poor guy might being going through Sanity Slippage himself.
- The mutated mako-infused human experiments created by Hojo found in Nibelheim's basement are in-verse Nightmare Fuel since seeing them causes Sephiroth, a being infused with high amounts of mako energy himself, to question if he's a monster. His quote after seeing them shows how horrified he is by the whole thing. Genesis' reveals about his birth only serve to push him over the edge into insanity.Sephiroth: Am I the same as these monsters? I knew since I was a child I was not like the others. I knew mine was a special existence. But this.. this is not what I meant! Am I a human being?!
- Crisis Core recreates the game's famous Nibelheim disaster with better 3D. And a Spooky Painting of a girl in Zack & Cloud's room. Despite not doing anything (that we know of) walking up to it prompts you to push X to examine it. Whereupon Zack will comment on how creepy it is. No other paintings in the room are considered noteworthy enough for examination.
- Sephiroth's Kubrick Stare and Sanity Slippage during the disaster is nothing to scoff at either. He goes from an aloof but clearly friendly and warmhearted friend to a ruthless and crazed madman rambling and laughing about his newly found alien monster mother, being superior to humanity, and calling himself a god destined to rule over the planet. All because he found out too many awful revelations about being a lab experiment and unable to decide if he was even human anymore.
- Genesis is pretty creepy himself considering he went from wanting to be hero like Sephiroth to a rambling Mad Artist wanting to gain the Gift of the Goddess to stop himself from degrading into a sludge pile due to being a failed experiment. You can see his pallor getting more and more faded and even force feeds one of his minions some of Zack's hair in a desperate bid to find a cure. It does not work and simply mutates the minion into an even freakier monster.
- The Genesis Copies. These were SOLDIERs, regular guys, that got injected with just a bit of Genesis' cells, stuffed in Mako tanks, and get turned into mindless drones, stripped of everything that give them their individuality, even their physical appearance, in a process that is potentially very painful. Gah. Made even worse when you think that, when Genesis first deserted Shinra, the SOLDIERs he took with him came of their own free will out of loyalty to him and they were the ones that wound up as the Copies. And some fans say Genesis isn't that evil.
- The Body Horror these Copies go through is pretty weird and creepy to watch since they are literally shown to be pale twitching silent creatures with small wings growing on their bodies and spastic movements.
- In the final mission and also the final area of the game (Banora Underground), you can see a shoulder of Emerald Weapon sticking out of a large formation of crystal.
Nightmare Fuel / Crisis Core
Considering this game is a prequel detailing the events that led to Sephiroth's fall from heroism and descent into insanity as well as Cloud Strife's eventual mental breakdowns, there's plenty of horror to go around.