I was wondering about that too. From my understanding (along with some reading up on the wikia), I think you (Solid Snake) still "kill" the real Big Boss in MG2, since he takes back over after Venom gets killed in MG1. Then Zero gets a hold of his almost lifeless body and preserves what's left of him in an artificial coma, up until MGS4, when he's released from it after The Patriots system that held him in that coma, is taken down or whatever. Then Eva and whoever else, put him back together fully using parts from Solidus and Liquid. So from MG2 to MGS4, it seems he was basically non-existent. Then he came back and died of old age shortly after.
....see if im still a beast
literally on the jungle map both teams were engaged in a huge fire fight and on one was fultoning people...we were down like 30 tickets until I fultoned out a 10 bounty and a 19 bounty and brought us back. I need to just go ahead a buy a mic...
