Free Will and Defiance, (Cut Content, Part 1): Defying History and Politics
Nuclear weapons figure heavily in the Metal Gear Solid series, but the anti-nuke talk was never as heavy handed as in this game. The conversation with President Baker was an extended discussion regarding the storage of dismantled warheads as they leak radioactive waste and the military-industrial complex, and the upcoming conversation with Otacon will detail how nuclear weapons can be safely tested in VR environments and the relationship between advancements in science and weaponry. At the end of the game, text appears informing us:
In the 1980's, there were more than 60,000 nuclear warheads in the world at all times. The total destructive power amounted to 1 million times that of the Hiroshima A-bomb.
In January 1993, START2 was signed and the United States and Russia agreed to reduce the number of deployed strategic nuclear warheads to 3,000 to 3,500 in each nation by December 31, 2000.
However, as of 1998, there still exist 26,000 nuclear warheads in the world.
On their own, the anti-nuclear themes in Metal Gear Solid made it boldly political for a game intended to be a huge commercial hit in the United States only seven years after the end of the Cold War. However, the discussion of nuclear weapons are also in part a metaphor for Snake's own past, a past he'd rather forget. In the same way that "there's still no real way to dispose of this stuff," and they just "close the lid and try to pretend it'll go away," Snake up to this point has been unwilling to address the unshakable truth of what he has done and what has happened to him in the past. This is at least in part why this portion of the game, so concerned as it is with uncovering the history of it's characters, takes place in the Nuclear Warhead Storage Building, since everything that happens here and much of what happens immediately after is dedicated to digging up these characters' histories.
In the same way that the game pans out with it’s observations of Snake’s character, we can apply the same ideology to the presence of nuclear weapons in the game. To deal with nuclear weapons, to disarm, we must confront the history that created them. Later games in the series would be more radical about what that would entail, as the games come to espouse not just a personal pacifism, but a radical political pacifism as well, a pacifism that might even be anarchist in nature.
-Austin C. Howe, Maryland, 2013
 I cannot verify this claim as of 1998, however, according to the Federation of American Scientists, there currently exists 17,000 nukes in the world, some 4,300 of which are operational and deployed, ready to be used as soon as the command is given. http://www.fas.org/programs/ssp/nukes/nuclearweapons/nukestatus.html
 This is also in part why the game takes away your weapon usage on the first floor, as a sort of metaphorical symbol of this journey into the unacknowledged past.