You mean the "brilliant" game about an AI system designed to censor the net that decides the best course of action to test his net-censoring abilities is to sink two tankers , one filled with oil , the other filled with marines, so he can frame Solid Snake for the deed ... Then allows a mentally unstable cowboy with split personality disorder to hijack some badass nuclear super weapon for the next part of their very elaborate plan. Already very credible as a setup.
They that AI proceed to spend the next couple of years building a bogus facility that doesn't clean Manhattan bay, instead they use it to build a gigantic battleship underneath. Then they try to coax a fringe group of terrorists into hijacking the facility, to capture the president and to gain nuclear capacity. But it's all part of their "brilliant" plan, of course.
Now they can finally test their net-censoring prowess by coaxing Raiden, an unstable recruit with personal problems, into completing a mission, by the power of ... a Colonel Cambell AI that has the gift of being able to say "Raiden, you must complete your mission" to motivate raiden, and with the help of his naggy girlfriend .
To test the boy's progress , they hire... A fat man ... on rollerskates to put live bombs all over the place, bombs which can blow everything apart if the young recruit fail. But the recruit manages to disarm the bombs, mainly because of Pliskin's involvement, although he was not "featured" in the simulation. That's right ,he would have failed without Pliskin... But let's ignore that.
In the end , their plan is a "resounding success". I mean, it's of no consequence that the president is killed during the mission , the big shell is destroyed and the oil gets spilled back into Manhattan bay , that Arsenal Gear crashes into Manhattan (hope your net censor program works, cause you got some heavy censoring to make everyone in New York forget about that ship that blew up half the town) . Remember how the revelation that the US had been developing REX created a huge international incident ? Now the US will have to explain to the whole world how they were developing a gigantic nuclear submarine city and it got hijacked by terrorists ? But the mission is clearly a success , because AI Cambell managed to make a recruit finish his mission by giving him basic orders like "Raiden, you must disarm the bombs". Clearly, this will help tremendously in terms of building the program's ability to "create context" and censor the net. Clearly, MGS2 is the pinnacle of video game storytelling , a subtle masterpiece of coherence and brilliance that is the equivalent of the best works of modern and antique literature.
There's a reason why the events of MGS2 aren't really mentioned in the rest of the series, and why Kojima ran back to the 60s and back to Big Boss's tale after MGS2... He had no idea how to salvage that plot. And as much as he tried to do something coherent with MGS4, the harm was done and imho, the modern day timeline was forever altered out or relevance due mostly to MGS2's nonsensical plot.
But alas, I'll give credit where it's due. The sheer surrealism of the premise, setup and exposition creates an interesting feeling in regards to how the players feels. You question what you are experiencing, if any of this is real, trying to find meaning to it all. In that regards, the game does feel post-modern, an an experiment about what it feels to be a gamer, playing a character and being coaxed into achieving something, forced to continue, not really knowing who you are, why you are fighting and so on. As an experiment, it works, especially the end sequences where reality starts to fall apart, and honestly, if the game would have ended being a VR simulation all along, it would have been a great game, but the fact it's actually part of the canon of a series that prides itself on it's storytelling really bugs me to no end.
Sinking a tanker, destroying half of Manhattan, doing all of this would have made sense if it was Raiden being strapped into a VR chair experience a "Solid Snake simulation". Sadly, Kojima didn't want to make sense, so he made the events happen in his real canon story, which imho destroys the canon's integrity... Well, it was the first step in destroying the integrity (we got signing mechs more advanced than Ray in the 70s nowadays).