The changes to Metal Gear Solid 2 as a result of the terrorist attacks on 9/11 are well documented, best known is that scenes of Metal Gear Arsenal crashing through New York were severely toned down. A good call, considering the game came out a mere 2 months after the event.
Less well known is that the Rockstar team had to change things to their upcoming game as well, Dan Houser goes into more detail in a rare interview with IGN.
"I think one mission got removed. There was a non-interactive jumbo jet, just to give some life to the sky, that looked like it could pass through a building. That got adjusted, and a few lines of radio dialogue in the talk show.
"The only other thing that changed that not really many people in the U.S are aware of, is the box. So there was an old box that you can still see online because it was the packaging in Europe. It was the same drawing style but done like an old movie poster with a blown up bridge and some police firing in the air and some helicopters and a bunch of the characters are different sizes. We thought, "that's a bit heavy, actually, it doesn't really gel." And so the artist came up with a couple things, and he just came up with a new one overnight. What's become the very staple of our marketing and presentation was done in an evening as a response to 9/11."
