During the mainline of the game you are an anti terrorist specialist sent to rescue the president from a bunch of stereotypical mad bombers
Well, basically, the leader of the terrorists is the 43rd US president, who is a clone of a super soldier despite being ostensibly anti cloning in office. (Yes, he's Dubya). He's planning to detonate a nuclear weapon above Manhattan so an EMP field knocks out all communications. The reason being that the government has been taken over by a conspiracy called the Patriots who are using a sinister AI to filter all internet traffic
However Dubya has been double crossed by an old Russian guy who was infatuated with the super soldier Dubya was cloned from. He claims to be representing the Patriots but suddenly his arm comes to life, claiming to be Dubya's brother. Oh, by the way, he lost his arm and got a transplant from the body of the other clone, Dubya's brother. It's implied in this game to be a supernatural occurrence.
Ghost Dubya 2 (in the body of elderly Spetznaz guy) goes on a rampage and tries to kill everyone. Dubya and the anti terrorist specialist end up fighting on top of Federal Hall, which if you've ever been to Manhattan is just next to the NYSE and TJ Maxx.
When you're there the Patriots phone you and they claim to be dead. Well, not dead exactly. They claim that in the same way life emerged from organic chemicals, life has emerged from the neural net of ideology and content published on the internet. Kind of like if ChatGPT became a bit uppity. They claim that Western Civilization is too corrupt and contradictory to be left in the hands of humans. You have to kill Dubya who is somewhat of an anti hero and it's kind of sad
Eventually another brother of Dubya who is kind of the hero does some digging, and his bromance partner discovers that the Patriots were real people but they all died 100 years ago. Also they were funding the real heroes all along!
It makes a lot more sense in MGS4