It's long been believed that the Joker would one day kill Harley Quinn, but the way he finally did it when he was Emperor Joker is the opposite of what readers would expect. The relationship between the Clown Prince and Princess of Crime has been a turbulent one to say the least. The Joker has notoriously abused Harley both physically and mentally for his own personal gain. This has led to the now iconic shift in Quinn's character when she breaks off from the Joker and forms a new name for herself, instantly becoming a household name with DC Comics. However, there was a point in her comics history when Joker finally ended up killing her before she left him for good...and the reasoning behind how he does it will shock comic readers.
It all happens in the Emperor Joker storyline by Jeph Loeb. After acquiring the powers of Mister Mxyzptlk, Joker has basically acquired a god complex as he can do basically anything. One of his biggest intentions is to wipe out all of reality, which will put an end to his chaotic rule. In a way, Joker is basically seeing his unlimited power as the problem with the universe, and he sees him extinguishing all life as a way to leave "behind a clean, quiet universe." He doesn't want more people like him to have such power, so he'd rather strip it all away than risk anyone else ripping up order with unhinged chaos.
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When Harley approaches him about his plan though, an unexpected side of the Joker takes form. She asks him if she really has to die too after being by his side for so long. When Joker brings her in for one last kiss, she fades from existence and turns her into a constellation in the sky, telling her this is her reward
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