Let me be honest with you:
There is no real issue here unless people choose to create one. This is simply morality by the numbers. Sacrifice a few, to save a lot. Anyone who has an issue with this needs to examine their priorities when dealing with the big picture.
No it's not a nice, or GOOD thing, that's the entire point. The entire situation is very gray. The big question is "would you kill a bunch of innocent civilians to maintain or establish a cover so you could save millions". There is only one answer to that question and it is "yes". If you answer no, then basically you fail and take society down with you.
The fact that it's an ambigious thing is what makes such a question, and it's proper answer, such a powerful act of storytelling in MW2.
I also can't help but wonder if Infinity Ward bought this contreversy, because honestly I expect more of article writers on The Escapist. Let's be honest, this is not carnage on any kind of unprecedented scale, nor is it anything paticularly shocking to target civilians. With the amount of time "Grand Theft Auto" has been around, I expect better from anyone who is an expert on gaming. In MW2 you at least have a reason for what your doing, and it's for the greater good. In Grand Theft Auto, or Saint's Row, your motivation pretty much comes down to "your a murderous, criminal, psychopath". Trust me, Saint's Row 2 was a LOT worse when your mass murdering homeless people so you can move into their squat on the morality O' meter.
I wrote another long message on the subject, but let's also consider that with MW2 the fourth wall is intact. There is no confusion with this being real, it's all 100% fantasy and hypothetical. Compare that to say rap music where there really isn't much of a fourth wall given what is said before and after songs during concerts, and the whole "keeping it real" thing where the performers try and sell the lifestyle and flaunt their criminal activities, convictions, and jail time as examples of how real it all is. When you see artists feuding about whether or not one of them REALLY killed anyone or did jail time, hustled drugs, or who was on whose turf... well you've got issues. Truthfully people DO criticize this, but if you want to pick at where a lot of violence comes from, that and other industries where there is no "fourth wall" are the place to start. At least with MW2 even the worst of it is for the greater good, there is no real way you can make some of the things rap performers have done and use to promote themselves benevolent, even in a big picture.
... Now excuse me, I guess I'll go rev up Prototype and run over several hundred civilians in a tank while still having the pretensions of being the good guy. Maybe I'll pause at some point to reflect on how nobody has slaughtered civilians before Modern Warfare 2, and how obviously a fantasy about an undercover CIA guy doing bad things for the right reasons is a much worse fantasy compared to being a vengeful totally sociopathic supervirus who eats people.
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Also let me be honest, the guy at Slashgamer dropped the ball on Fox News, and I think it was set up, but understand Fox News gets criticism for showing both sides of a story, even when it's not politically correct. It's early in the game but I expect them to come down more in favor of video games and such than against. Really it's the left wingers from CNN and such you have to watch out for because they are the ones with "their" politicians in power who are also on a censorship kick.
You can't really knock Fox without knocking other networks here, and honestly at the end of the day I half expect them to come down on the free speech side. I could be wrong, but as I said it's relatively early.