After the events of Metal Gear Solid 3: Snake Eater, Naked Snake isolates himself from the United States and sets up home in Colombia. Here he creates Militaires Sans Frontières, a private military group that provides support for countries in need. But at the same time, an unknown army of well-equipped soldiers has taken over the defenseless country and brought along a nuclear warhead labeled Peace Walker to demonstrate their power. Naked Snake is asked by the government to save the country along with his Militaires Sans Frontières.