Basically, the initial setup was this: Green Lantern -- doesn't matter who, might as well be John -- is patrolling Sector 2814 when his ring detects an approaching starship. It's an advance scout for a massive armada headed, yes, straight for Earth. Naturally, GL alerts the Justice League and also buzzes Oa for backup. The JLA is prepped and ready for action, but the word comes back from Oa: reinforcements denied. In fact, a Guardian gets on the horn to tell John specifically that he is to offer no resistance to the invaders. Instead, he is to observe and advise them. He can protect the Earth's best interests, but the Guardians have determined that the invasion must be a success, because that's the only way Earth can survive.
John then contacts the JLA from aboard the invading scoutship and explains the situation. Obviously John is conflicted, but ultimately he has no reason to distrust the Guardians. Besides, he (and presumably any other Green Lantern in the area) will theoretically be able to influence the invaders in Earth's favor. Of course, the JLA and the rest of Earth's super-folk have no such conflict, and while there is some debate over whether to follow John's lead, eventually the choice is made to repel the invaders.
Thus, the stage is set: hundreds (if not a thousand) hostile starships bearing countless troops, versus the Justice League, Justice Society, Teen Titans, et al. There are pitched battles in orbit and fierce fights on the ground, but the invaders eventually get past the superheroes. The invaders seem to be looking for something, but they don't know quite where; and they tear the dickens out of several regions in the process. Cairo, Helsinki, Nepal, and Salt Lake City are hit especially hard. Regardless, thanks to John, casualties are amazingly low, including among the superhumans. Indeed, the invaders start ham-fistedly rebuilding the infrastructure of the devastated cities, even advising local leaders on alternative forms of government.
Once the invaders believe Earth has been subdued, though, the JLA and its allies strike back using guerrilla tactics. This is quite successful, in part because the invaders are caught off-guard. Before they know it, they've lost half their fleet and most of their infantry has been incapacitated; and they're ready to retreat. After Green Lantern has escorted them out of the solar system, he gets a call from Oa: the Guardians are pleased.
Pleased?!? John spits. You could have stopped all this before it even started!
Yes, muses the Guardian coolly, but the [invaders] needed to be taught defeat. The Guardians knew that bloodying the invaders' collective nose was the only way to get them to leave Earth alone, but calling in the GL Corps would have merely turned the invaders' attention to Oa. It seems the invaders are a particularly thick and brutal race, but one thing they do especially well is fight -- so they would have first found a way to eliminate the GL Corps, and then they'd have come after Earth. And make no mistake, John Stewart, intones the Guardian, [the invaders] would have dedicated their very existence to wiping us out. Now, however, they see that even if they defeat an enemy one day, it also won't stop until it's driven them off. The Guardian wraps up by saying they regret having to manipulate John and the other Earth GLs as they did, because (irony alert) they normally don't work like that.
* * *
Now, clearly there are a number of problems with that story. I first thought of it when I was half-asleep, and I fleshed it out on the fly just now. The point, though, is that it is a blatant morality play about the Iraq war, and I'm not sure that something as deadly serious as Iraq (or Afghanistan, or wherever else the U.S. finds itself) should be trivialized, even potentially, by adapting it to a superhero setting. For one thing, it's designed to leave no lasting scars on the Earth or its people. For another, the invaders are pretty one-dimensional -- they're looking for WMDs because they think someone on Earth attacked them, but that's never really made clear.
Still, if you declare that some subjects are off-limits to superhero stories, aren't you shortchanging the genre? Joe Kelly wrote a decent Iraq-related issue of JLA, where President Luthor basically lies to the Justice League to get them to invade an inoffensive country; and Greg Rucka put Lois Lane in harm's way in "Umec" during his tenure writing Adventures Of Superman.
I actually do like the story, mostly for the moral dilemma it puts GL in. I suppose you could strip out the more obvious real-world parallels and make a passable 2- or 3-issue arc out of it. It wouldn't have any real-world lessons, but it might be entertaining, and it would definitely explore the relationship between a Green Lantern and his little blue bosses.
Still, on balance I'd like my comics to be open to larger moral concerns. I'd just hope they'd be able to get past all the fantastic stuff.