Maybe with the source code, I'd be able to figure out what the hell happened in the last ~2 hours of the game.
Not much, just accurately predicted the next 30 years exactly
Try the classic analyses: https://www.deltaheadtranslation.com/MGS2/ and https://www.aumaan.org/form1/tus1/features/dreaming1.htm.
Dunkey MGS Explained https://www.youtube.com/watch?v=aaLiLRVeaZA
Kojima saw the writing on the wall so speak, and told us what the future held in a series of metaphors and dense monologues.
My favorite tidbit of the series (but it's in Metal Gear Solid 3): in the torture scene where Volgin interrogates Snake in an attempt to discover who is the spy in his ranks, of all the persons present in the room (and if I got everything right from memory):
- Volgin is not an agent
- Snake is an agent (USA spy)
- The Boss is a double agent (Soviet/USA spy)
- Eva is a triple agent (USA/Soviet/Chinese spy)
- Ocelot is a quadruple agent (GRU/KGB/CIA/Philosophers spy)
And of course, after that Volgin then kills Granin thinking he was the spy, but he wasn't.