[Nowhere Man]

If I remember correctly, that episode was while Lex Luthor was pretending to be reformed and was running for President. As part of his whole "hey, I'm not a would-be-dictator supervillain anymore" image, Lex was unveiling a new city powered by some awesome free-energy source, and got Captain Marvel to endorse him, since he's even more of a 'boy scout' than Superman.

Supes naturally doesn't trust a damn thing Luthor says, and assumes that the whole thing is some kind of trap, which is confirmed when he sees that ticking time-bomb at the end of the video. He starts tearing up the place to get to it, Captain Marvel stops him, and they end up throwing down. The twist, then, is that the "bomb" Superman melted down was actually the generator for the city's power (made to look like a bomb so he would destroy it ), making Supes look like the bad guy and causing Marvel to quit the Justice League altogether. Basically, Luthor played them both for chumps in order to ruin Superman's image, like the magnificent bastard he is.

Which kinda goes back to the argument about Supes being "overpowered" being rubbish- guys like Luthor or Brainiac (or yes, like Batman) can put him in situations where being able to punch stuff really hard doesn't do him any good, where winning the fight still doesn't solve the problem. The guy can be duped, tricked, and humiliated, just like anyone else, without a speck of Kryptonite in sight.