Most likely as a deterrent.
Metal Gear Solid V: The Phantom Pain will give players the option to have their own nukes. This is kind of expected since players will take up the role of Big Boss, who is the main villain of the series and since the game may tie into the events of the original game, this is no surprise that Big Boss may be using the nukes as a deterrent.
“At this point I give the player the option to think about acquiring a nuclear weapon, in order to deter these attacks, a kind of threat. It illustrates the cycle of nuclear weapons, what inspires people and nations to enter into that system. It’s something that you can only really do in video games,” Kojima said in an interview with The Guardian.
It will be interesting to see how this will tie up with Motherbase and whether we will be able to customize the nuclear weapon, just like Zeke in Peace Walker. For more on the game check out our hub page here.