So you catch up with Skull Face, and he gets what's coming to him. The story and 'weapon to surpass Metal Gear' is a parasitic virus that latches onto the vocal cords of people, and when they speak a certain language, they die. Skull Face was gonna commit mass genocide and kill everyone that didn't speak English.
So MGSV is more about biological warfare than nukes and Metal Gears themselves. I wasn't too invested/bothered by his motives. Probably due to lack of seeing Skull Face much, not a lot of character development for him, and his voice actor which I didn't think was fantastic.
There was this whole seen for like 10mins of Snake and Skill Face traveling in a jeep with Skull Face telling Snake his big plan and Snake sits there the whole time saying nothing. The scene felt so dead because of that. Then half was through Skull Face shuts up and the 'wwwhhoooooaaaoooo' theme song plays while they are both sitting and starring at each other silent. Was really stupid.
Then the song ends an Skull Face just does some more talking. Very uninspiring.
Anyway, the giant Metal Gear Sahelanthropus gets taking over by the floating gass mask boy (Totally child Psycho Mantis) and you fight it. It's the first actual boss fight of the game, and for me this was at the 50 hour mark (I've been doing lots of side ops etc. though, you can encounter it way earlier if you are doing just 'story' missions).
After the fight, you go deal with Skull Face:
Note that this isn't a cutscene, and you can pull the trigger as you wish to finish him off. If you wait (like I did) Snake has a flash back about everything Miller and himself have lost, and then he proceeds to blow Skull Face's arm and leg off as revenge for Miller. It's badass and gruesome.
Huey then pumps the last bullet into his head while Snake and Miller walk away. Brief rant about Heuy: They made him even more of a whinny little bitch in this game and it looks like he's the biggest traitor on Mother Base. I loved him in Peace Walker but now my memories are gonna be the traitor him that destroyed all I made :(
Anyway, mission cleared:
In my opinion (and as proved right here) Sahelanthropus was a piss easy boss fight. Had alot of potential but fell short for me as a really decent boss fight. There wasn't any stress really, nor real motive to take it out (besides the usual 'It's a Metal Gear that will destroy the world'). Not like the Peace Walker boss fight anyway..
It was an insane fight though, and Sahelanthropus was freaking giant and had like a whip of doom that ripped up the ground and a railgun that always 1 shot killed me.
I got an instant S rank and the only points I lost was from taking 4 hits:
After the fight and killing of Skull Face you return to Mother Base and rewarded with actual cutscenes. Glorious ones too. Miller did a sweet monologue as you walk from the chopper:
Kickass men being kickass.
Helicopters then literally deliver Sahelanthropus to Mother Base and it now lives on my R&D platform. Really awesome scene:
Snake says something along the lines of this is what Diamond Dogs will be remembered for, and what their achievement is. They can all remember by looking at it.
Cutscene ends with Eli being given the last vial of the vocal parasite from the Psycho Mantis kid, and he just stares at Sahelanthropus so he's gonna try to screw my shit over obviously.
All guesses about characters people made before the game was out were pretty much spot on too. Man on Fire is Volgin from MGS3. Eli is totally young Liquid Snake. Psycho Mantis kid is Psycho Mantis. Quiet is the chick from the start who tried to kill the boss.