Maybe with the source code, I'd be able to figure out what the hell happened in the last ~2 hours of the game.

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.

Not much, just accurately predicted the next 30 years exactly

Try these classic analyses: https://www.deltaheadtranslation.com/MGS2/ and https://www.aumaan.org/form1/tus1/features/dreaming1.htm.

I need scissors, 61!

Kojima saw the writing on the wall so speak, and told us what the future held in a series of metaphors and dense monologues.

Dunkey MGS Explained https://www.youtube.com/watch?v=aaLiLRVeaZA