Let's be honest here, the Metal Gear Solid saga is hard to follow. Fascinating and intricate, sure, but like a daytime soap with clones, nanomachines and mechas.
Don't worry if you are baffled at times. Series creator Hideo Kojima gets baffled, too, scratching his noggin while figuring out plot points.
"I personally get confused too about the whole timeline and saga of Metal Gear Solid," Kojima told game site Eurogamer. "This is especially tricky when you create the future first and then go back in time to create something new. There are a lot of small aspects where sometimes it doesn't match completely."
Konami's Hideo Kojima Interview [Eurogamer]