The scene where Amadeus Arkham found the mutilated bodies of his daughter and wife in an upstairs room, who were murdered and raped by the Serial Killer Martin "Mad Dog" Hawkins. Arkham found the head of his daughter inside her Doll House.
What makes it worse is that afterward, Arkham ate their bodies.
The portrayal of villains like the Joker and Clayface, who in this comic appears as a naked man whose skin is literally wasting away and who wants to "share" his disease.
The scene where Batman breaks Clayface's leg when he tries to "share his disease" with him.
At the beginning of the story, a young Amadeus Arkham brings his mother's dinner. The old lady responds, "I've eaten," as beetles fall out of her mouth.
The scene where Batman fights Killer Croc and the conclusion where he is forced to impale Croc with a pipe to drive him back is extremely intense and very disturbing. It's easily one of the most visceral scenes in the book, which is really saying something.
The incredibly disturbing version of The Scarecrow, who drags a pitchfork along a hallway with spastic movement as Batman observes from the shadows. This version isnt portrayed as a fear obsessed scientist either, but as Morrison himself observes, instead represents the creeping horror a scarecrow awakens in human.
Maxie Zeus is a madman with severe messiah complex and electrophilia, based on the insane Earl from The Ruling Class. When Batman finds him, he is hooked up to an electroshock machine, continuously feeding off the electric current. He also suffers from coprophilia, hinting that an oak bucket contains his own fecal matter that he thinks will bring life to the barren Earth
Dr Destiny is no longer a creepy but somewhat cartoonish man in a cloak and a skull face. He is an emaciated, withered man trapped in a wheelchair. Its implied that he still posseses his terrifying dream powers as well
The implication that Gotham City, Arkham Asylum and all its inhabitants may be in some sort of stable time loop, and that Batman may be the bat spectre that drove Arkhams mother, and eventually Arkham himself, insane. The Bat creates Arkham, Arkham creates Gotham, Gotham creates Batman, and so it goes...
In the climax of the book, Dr. Cavendish has Batman by the throat, screaming "MOMMY'S BOY! MOMMY'S BOY!" This, coupled with the hell Batman has been throughout throughout the book, totally breaks the Dark Knight—he's completely helpless (ultimately, Dr. Adams kills Cavendish with a razor). There's something horrifying about seeing Batman—an archetype of The Stoic and someone who would later fight a successful battle against Superman himself—so utterly broken that he can't fight back against a skinny nutcase, something Morrison acknowledges in his script. Batman—Batman—nearly died. That's terrifying.