The story is a convoluted mess of insanity and retcons even when you're played the games, really. I've found the best way to enjoy it is to just go along for the ride and laugh at all the really goofy weird shit going on (and also Snake being a clueless goof all the time).
Try to get to play the originals. Do you have a friend who could loan you a PS3? Or, hell, if you've got a bit of extra cash, the things don't cost a whole lot these days and are likely to get even cheaper when the PS4 is released. MGS1 and the HD collection are really solid buys, even if I think 2 and some parts of 1 haven't aged very gracefully.
And yeah some people say the MGS2 PC port was ok, but my experience with it was straight up terrible. You only got to access controls and shit through the launcher, the controls listed buttons by what PS2 button they corresponded to instead of by function, and every time I closed the game while figuring out the mess of the controls I had to force quit the application since it failed to close properly. I quit after like half an hour, before I had the controls set up.