There we go.
Yeah, reading through this thread, I'm just gonna go with "don't pay that much attention to MGS5's story". Or maybe just "don't pay much attention to MGS5's story after the first ending
", but it's all kind of a shaggy dog tale before that.
And much more of one afterwards.
Might as well try to untangle this mess though.
The "Truth" mission makes this a little clearer... maybe. In the prologue proper you're shown the player-generated face at first, with the doctor stating that it's the face he gave you, and then you see the Big Boss face and he calls it a "phantom". What you're meant to believe is that the Big Boss face you see throughout the game is only Venom's self-image; to everyone else, you look like the "altered" player character.
The player character was made to look like Big Boss before he ever "wakes up". The whole thing with them talking about how they are going to change your face is an other level of trickery. Big Boss wants everyone to think you are him. This way the lie that you are him and changed your face to look different, if they ever figure out that happened, they'll assume that's where the rabbit hole ends. It's convoluted, but thats Metal Gear for you.
In Truth, though, these faces are switched, revealing things for what they really are: The player face is Venom's original face, and the Big Boss face is what he was altered to resemble. That's what Miller and Ocelot and everyone else sees and recognizes. Venom remembers and sees his old face (rather than Big Boss's) in reflections, but he writes that off as normal, because he was told that that's just what he looks like now. The mission ends with him looking in the mirror and realizing for the first time that Big Boss's face really is his current, altered face.
Endgame timeline is fairly explicit that "Big Boss's phantom" gets killed in 1995, and Big Boss proper in 1999.
Everything in the wiki is still making assumptions, because you do get the tape for operation intrude N313, which heavily hints at you becoming Big Boss for MG1, but in MG2 Big Boss has cybernetic parts, which could easily make you Big Boss for MG2 in zanzibarland.
Interestingly enough, the conversations that follow suggest that Naked Snake is off quietly building the true Outer Heaven (somewhere in or close to South Africa, remember) while Venom's building Diamond Dogs in the Seychelles. So even though Venom shows up in Outer Heaven to get missiled in the face by Solid, it's not his country. The question of which one of them is acting as Solid Snake's CO is kind of left hanging, and that bugs me a lot because it's the single biggest question I wanted MGS5 to address: how does a known nuclear terrorist manage manage to go back to heading an elite paramilitary unit for the CIA???
My best guess is that it's Naked doing that too, because he's got a neat cover: since he is the genetically provable Big Boss and now there's some other asshole out there using his likeness and his name and doing all of the exact same shit he did in the Caribbean - building a private army on a converted oil rig, hoarding nukes, sending a god damned Metal Gear out on petty dispatch missions - he can be like nah man that wasn't me in 1974 it was this Venom asshole, gimme some sneakmans and I'll stop him. So that's how Big Boss can be on the radio at FOXHOUND HQ and also be holed in in a little room 200 miles north of Galzburg - he just phoned up Venom Snake and was like YEAH HEY SO I'M GONNA BE FUCKING AROUND WITH THIS CLONE OF MINE FROM HERE SO I NEED YOU TO GO POSE AS ME IN OUTER HEAVEN I PROMISE YOU WON'T GET MISSILED IN THE FACE TO DEATH OR ANYTHING and Venom Snake is just like YEAH SURE THAT SOUNDS COOL because Venom Snake is a god damned tool.