- Why did Jokers obsession over Batman and his inability to forget about him mean he lost control over the universe? The idea seems to be that if he could not do all things, then he could not do anything, but why is that the case? Why does that one limitation strip him of all his powers?
- It seems to be a case of Your Mind Makes It Real. Basically, Superman pointed out that for all of his amazing abilities, the Joker couldn't do the simplest thing of all—permanently kill a single, non-superpowered individual. No matter what he tried, no matter how many tricks he pulled, the Joker couldn't do something phenomenally easy. The realization of that weakness led the Joker to start doubting his own power, and by doubting it, he lost any ability to control it.
- Also, it's worth remembering that he technically never had all of Mr. Mxyzptlk's power; just 99.9% of it. So presumably since Mxyzptlk still had 0.1% there was still a connection between the two of them. Reminding Joker of just how deep a hold his obsession with Batman has over him undermined Joker's control over the 99.9% since he'd reached the limits of what he was able to do, which enabled Mxyzptlk to start draining his power back until it was all gone.
Headscratchers / Emperor Joker