I wonder how they must have felt to have coded a 9/11 scenario of Arsenal Gear crashing into the Twin Towers, and then watched it actually happen a few months later.

This was cut from the game but is still in the source code leak, just commented out! https://www.youtube.com/watch?v=DNSPx-oRV60

Also note that the source code was leaked on April 30th :p

Everyone focuses on that part, but what the hell was with the girl that could repel bullets but it turns out that it was magnets but actually maybe she does have powers? And what about the weird thing where you start sword fighting your father/president/clone?

Yeah I know, sure, fake information on the internet. It's so prescient I guess, but the actual story is incomprehensible.

Including the cardboard boxes: https://taskandpurpose.com/news/marines-ai-paul-scharre/

Surveillance states and mass media manipulation are a staple of sci-fi. Those topics were particularly common around that time too. E.g., The Matrix.