Warning: Explicit Content
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In the comics
In the comics, rape is a subject that is referenced a number of times, whereas on the Super Friends, due to censorship, it's mostly subtle references, in the comics it is directly mentioned. Batman was raped by Talia, and that's how his son Damian was born. Doctor Light was also a rapist, and he raped Sue Dibney, Elongated Man's wife.
The Joker has also raped several people. He may or may not have raped Barbara Gordon in The Killing Joke, since he took naked pictures of her and there was blood around her genitals. In Batman Cacophony, he says that he wants to “defile Batman’s corpse sexually”, which is necrophilia.