@MichaelRD777  
It’s an explination for how Big Boss survived the original Metal Gear and appeared in Metal Gear 2: Solid Snake, back before “Solid” got tacked onto the franchise name.
 
And honestly, that kind of thing is what does more damage to Phantom Pain’s plot than anything else. I think the people at Kojima Studios realized when Konami started restructuring what was going to happen, and so made Phantom Pain the capstone to the Metal Gear franchise. As a result, the story was written to tie up as many dangling plot threads as it could, up to and including how Big Boss survived the original Metal Gear. And yeah, it’s stupid continuity BS for long-time fans of the franchise, but…well, I honestly appreciate the sentiment, if not the effort. It just means you have to look at Phantom Pain’s plot from a franchise-wide perspective, not as a stand-alone game.
 
And besides, Hideo Kojima always did love his little plot twists, even 29 years ago. After all, Big Boss being the man behind the villians in the first Metal Gear back in 1987? Yeah. Nobody saw that coming.

Kaz… I’m already a demon.

Kaz…………you can’t play a fiddle with hooves.

@WrenchMan  
Yeah, TPP’s Snake turning out to be the friggin medic from Ground Zeroes is definitely a bunch of ass that ruined the story, IMHO.

@MichaelRD777  
And Snake’s ass…  
Can’t forget Snake’s ass!

Badass ponification is badass.  
A shame that the game that it’s based on is just… ass(in regards to story), though.

I’m already a pony, Kaz…