I wanted to replay the game to understand why Big Boss would start building the Metal Gear -- I mean, why would he repeat Volgin's folly? This is still not clear to me.
Though Big Boss states that he sent a rookie like Solid Snake so that he could return with false information, I do think that there's something else going on as well... He says: "I will not die for nothing. You will die with me. Come on!" Is Big Boss trying to pull the same stunt as The Boss did in MGS3? Did Big Boss know that Solid Snake was one of his sons?
At the very end, you see Solid Snake running away, and then a mushroom cloud blooming on the horizon. Then you switch to the radio screen, and Solid Snake sends out a report (to whom?), which end with the words: "Everything is over. Everything..."
Little does he know.