It all makes sense now

Naked Snake/Big Boss is a metaphor for Nuclear Deterrance (with a twist)

His second (The virtuos being his first (with Fox anyways)) mission is to prove America didn't attack Russia (on the surface atleast) with a nuclear weapon and in doing so had to face something much more dangerous the Shagohod a weapon that could fire a Nuclear weapon from practically anywhere (and forgive if I'm wrong it's been awhile since I've played 3) could by using thrusters on it's back section to effectively fire an ICBM from any runway long enough.

After defeating the shagohod he had to beat one more "weapon" one who's ideals could throw off the balance of the very idea of Nuclear Detterance iteself, The Boss (see games that take place chronilogical after 3 for evidence) if she had the time/chance to propagate her vision herself, with her own words beyond the few who heard her last words.

Peace Walker had him once again stopping all out nuclear war between the U.S and Russia. This time he and his PMC are hired to help out with civil unrest in Costa Rica and again "stumbled" upon some again much larger than previously thought. (that happens alot to his family) This time someone has found a way to weaponize detterance itself, largly in the form Metal Gear Peace Walker, an AI that is guarenteed to retaliate to a nucler launch. By taking the human element out of the equation he aimed to shift things in America's??? (again been awhile) favour by simulating a launch by Russia on America.

Big Boss by defeating Peace Walker/The Boss he was in effect overcoming detterance itself and became a global target in doing so. (having that nuke helped a bit to)

Than he went into a coma, putting detterance to sleep (for a time).

Now, he wasn't dettering nuclear war, he was a detterance against balance shifting. All his missions required him at the end of the day to "Maintain Balance". However just as Nuclear Proliferation which first started off initialy as detterance (just to maintain balance) and was probably not meant to go as far as it did, Big Boss became a viable threat to the world. Key factors in this where the size of his private army, the method in which it grew, and the missions they were taking on.

TL:DR

Big Boss's role is the maintainer of the balance that is necessary for Nuclear Detterance to work in the first place and in the process became a threat and a balance shifter himself

Edit: The TL:DR dat grammar though

Edit 2: Electric Boogaloo;Anecdotal evidence, https://www.youtube.com/watch?v=Tl9Pm0_1Mes but think about it.

(real) Edit 3: Fix a mistake or two

Random shower thought. What if the patriots are just a bunch of nerds who got too much money

Proof

Zero-James Bond

Para-Medic-practically all movies

Sigint-genius engineer and weapons specialist (war miniature games were made by and for these guys)

Ocelot-Furry Duh

Big Boss-The casual fan of things/absolute genius

Eva-Loves ramen, I don't know

Edit 3: It's all coming together https://www.youtube.com/watch?v=41U78QP8nBk

Edit 4: Hmm, getting ideas https://www.youtube.com/watch?v=5hyI_dM5cGo

Edit 5: https://www.youtube.com/watch?v=JManm091qWI

Edit 6: Has science gone too far? https://www.youtube.com/watch?v=94d_h_t2QAA