The Lord of the Flies has been interpreted several different ways. The most popular is that it refers to a state of existence where the one left standing is the lord of nothing but flies. To extend the metaphor imagine the flies that swarm around carrion. Nothing is left but dead carcasses and flies.
Golding wrote the novel at the beginning of the Cold War in the 1950's where the threat of nuclear annihilation was in most people's minds on both sides of the Cold War. The title is Golding's comment on the political situation of the time. He is warning the reader of the danger of winning the Cold War. It is a war where the winner wins in effect nothing but the fact that they have won.
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