While Jeph Loeb was writing Emperor Joker over in the Super-titles, Mark Waid had just taken over writing JLA from Grant Morrison. One of his earliest stories is one that highlights both the differences between Superman and Batman and the fact that they're a duo apart from the rest of the League.
The story of Tower of Babel is one of the ethical "hot spots" of the DCU, along with Zatanna's mind-wiping in Identity Crisis. The simple explanation of events is that Batman has been collecting data and formulating plans on how to take down each of his teammates if they're ever mind-controlled. These plans are stolen by Ra's al Ghul and Talia and used against the League. As a result, the League votes (in a close vote, with Clark as the deciding vote) to eject Batman from the League.
I've gone around and around on the ethical arguments about this one and my take on it is always hopelessly muddled (the short form is that Waid had to write everyone out of character to get his results--for starters, as the leader of the JLA, Superman would probably have insisted all this contingency planning happen anyway, just with consent, which would have dead-ended the whole story), so I don't have anything interesting to add about that.
What I do have are angsty, angsty scans.
Batman is fighting Ra's when he realizes what's happened:
Immediately he knows that al Ghul has stolen all of his plans on how to destroy the League. But who is it he starts crying out to? Sorry, Arthur, you rock but it's not you:
Batman totally just leaves anyway, by the way. I like the mental image of him hucking ninjas around the room by the handful.
The Kryptonite, by the way, turns Superman's skin transparent so he overloads on sunlight and can't function--non-lethal, but effective.
The League votes Batman out, with Superman's vote the deciding one. However, with Batman gone the League is dangerously weakened. In addition, the division between those who voted for Batman and those who voted against him is undermining team unity. Superman eventually realizes this can't continue, and he shows up in the Batcave for a heart-to-heart with Bruce.
What I like about the conversation (in addition to the visual intensity, just the two of them in the blackness), is the very strong feeling that these two men have a special connection that transcends the League. They may disagree on a lot of things, they may even be really angry at each other right now, but they know there's a fundamental relationship between them that trumps everything else:
Here Clark tells the story of the latest mission, which was nearly a failure due to a lack of trust, then comes back:
Mmmmm, hands. ^-^ Oh, right, the glasses. In this version of the JLA, no one knows Batman and Superman's secret identities but each other, so Batman's gesture is a very pointed one. And after some thought, that's what they decide on. The result is a just plain wonderful scene where Clark and Bruce "come out" to the League together:
Nervous, awkward Clark and sexy CEO Bruce together! *melts*
So Tower of Babel has its crazinesses and difficulties, but I can't help but love it just for Batman freaking out that Superman's in danger because of him, and the big civilian reveal at the end. Yummy.
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