- The Scarecrow's gas provides in-universe nightmare fuel. It's nasty stuff, often leading to horrific and recurring nightmares, long-lasting mental trauma, and Mind Rape. Victims frequently never recover years after the initial gassing, assuming they survive at all, which Crane couldn't care less about. He's subjected his own henchgirls, countless kidnapped civilians, and at least one child to this with no moral qualms and all For Science!.
- Crane's lair is not a nice place to be trapped in if you're one of the aforementioned abducted civilians. He's known to keep human test subjects trapped in cages like lab animals to be experimented on.
- Between street crime and costumed criminals frequently running loose and killing civilians with Arkham as little more than an inconvenience, Gotham City is not a nice place, especially from the perspective of a civilian whose bank gets robbed by Two-Face, or tortured by the Scarecrow, or is attacked by Mr. Freeze. And Batman isn't always around to help.
- While they're more Affably Evil than Crane, the girls have their nasty moments, too - in Tourist Trap, Techie deliberately lures an innocent girl into a trap to be gassed by Crane, and it's suggested that they assist him in rounding up "test subjects" for his experiments. At one point they flay someone alive just because he was rude. The only time they seem openly bothered by this is when Crane tortures Marilyn Keeny.
- The fate of Karen and Marilyn Keeny in Small World, crossing over with Tear Jerker. Karen is strangled to death by the Scarecrow, her own son, who then viciously decapitates the corpse and terrorizes her daughter Marilyn into insanity with her mother's head on a dish with wine glasses before forcing her to play croquet with it. Then he kidnaps Marilyn years later to Mind Rape her again. Captain, Al, and Techie are shocked and disturbed by the brutality of the scene, one of the few times that they question his actions. Crane only says that he could have killed her. And then he makes an aside about his father begging for his life and what he did to his other sister...
- While Crane's relationship with the girls and Kitten humanizes him to a degree, there are plenty of reminders that he is still a ruthless villain and callous Mad Scientist with no qualms whatsoever about experimenting on, torturing, or killing innocent people, most notably in Tourist Trap, Small World, and Hug It Out. While most of his worst actions take place offstage, Crane is at his absolute darkest in Small World, in which one of his victims is a child who he deliberately terrorizes into madness, and the story is told in large part from the point of view of another victim, their terrified mother. In general, for all the girls' glomping and calling him Squishykins, and despite his sympathetic qualities, Jonathan Crane is not a good person and crossed the Moral Event Horizon a long time ago.
- Crane's fundamentalist great-grandmother was horrifically abusive to him, both physically and psychologically, and is in large part responsible for how he turned out as an adult. What is seen of her in Noel, from a young Scarecrow's perspective, is terrifying.
- The circumstances that contributed to making Crane the way he is are also frightening on a more realistic level and depressingly believable: as a child, he was bullied by teenagers much older than he was, who were able to get away with it due to community neglect and personal connections. At home, he was subjected to his great-grandmother's physical and psychological abuse and neglect. The former is highlighted in The Paean of the Bells and the latter in Noel.
- What happened to K. Crow. She accidentally let the Scarecrow into her apartment, and he murdered her and her roommate just to take out his frustrations with Al.
Nightmare Fuel / The CATverse