I suppose this is a good time to post one of my crackpot theories. I posted this on a Metal Gear forum under ZERO PHOENIX.
This is what the MG series is shaping out to be in light of these new games:
Snake Eater
Portable Ops
Phantom Pain
Peace Walker
Ground Zeroes
At the end of PO Sokolov thought BB died in that explosion. We know that BB lived but he did lose his arm. We see this in PO's ending where one arm is a prosthetic. Of course in Phantom Pain it's the wrong arm that's missing but if we look at the time that would have to have passed within Portable Ops it would have been at least a month between BB stopping Gene and then being decorated by the U.S. government for saving the world. What if Big Boss got captured shortly after stopping Gene?
Look at this from the Portable Ops perspective.
Portable Ops - Snake stops Gene - Snake tries to stop nuke - Snake saves the day but is left comatose after the missile he's in impacts - Snake wakes up in the hospital we see in Phantom Pain - Whatever the hell happens in Phantom Pain happens over a few days - The crises in Phantom Pain whatever it may be is resolved and Snake is rescued perhaps by the U.S. government thus leaving the location of Phantom Pain - Now we see the ending of Portable Ops - Now we head into Peace Walker and then finally Ground Zeroes.
But what about BB's arms? Why does BB have two arms in PW? Simple. They cloned him a new one. The CIA tells Snake they have a way to restore his arm and do so by cloning one. They don't tell him that the cloning of his arm is in and of itself part of the Les Effants Terribles project. In fact, while BB was comatose his arm might have even been cut off for the Les Effants Terrible project. Anyway, the CIA sees how easily they are able to clone a part of Big Boss and then take it to the next level by trying to clone BB in his entirety, thus leading us the eight fetuses cloned from BB only for five to be aborted in the womb and the rest we know is history.
This is why Snake is missing an arm at the end of PO but has both arms in PW and GZ.
SE - BB's origin story
PO - Snake stops gene, Snake is left comatose after the missle fiasco, and somehow loses his arm.
PP - Those guys rushing in may be involved in the Les Effantes Terribles project. They could be looking for BB for the purpose of getting his body and cloning the greatest soldier ever to walk the earth. However while they're trying to extract an entire person i.e. BB someone else already made off with his arm. That someone else being the CIA. Somehow BB is rescued and we see the ending to PO.
PO Ending - Sometime after this ending and before PW Snake's arm is restored via cloned tissue manufactured during or after the events of PP.
PW - Snake has both arms.
GZ - Of course Snake still has both arms and is still completely unaware that the cloned tissue used to make his arm is part of a bigger project.