According to William Golding, Lord of the Flies is his "attempt to trace the defects of society back to the defects of human nature." To do that, he creates a setting and characters who should be able to maintain a civilized way of life even without the presence of laws or authority; instead, human nature takes over and all is nearly lost.
A group of English schoolboys is left stranded on an island after a plane crash; no adults survive, so the boys must figure out how to survive on their own, knowing that it may be a long time before they are rescued. It is the perfect setting to test the inclinations of human nature without any restraints or restrictions. Though they hold an election the first time they meet, the boys are certainly not well organized or committed to maintaining order.
In fact, part of the tribe--most of the older boys--spend their days hunting for pigs so they can have meat. For one of those boys (Jack), hunting becomes an obsession. Soon the island is divided into two unequal parts. Ralph is the leader of the smaller, more civilized group, and Jack is the chief of what Golding eventually just refers to as a tribe of savages.
Several boys are killed, one in an awful scene of disorder and another deliberately. When Simon, who represents the soul or spirit, dies, things begin to deteriorate more quickly. When Piggy is murdered, all intellect and reason (which he represents) are gone. That just leaves Ralph (the physical aspect of man) and Jack (the unrestrained human nature of man) to battle for supremacy, and Ralph does not have a chance. Every other boy on the island is now part of Jack's tribe, and he has ordered that Ralph be killed.
Just as it appears that Jack will get his way and establish supreme rule over the savages on the island, a naval vessel arrives (after seeing the conflagration the boys have set in order to flush Ralph from hiding) and the boys are rescued. When Ralph sees the naval commander on the beach, he weeps for "the end of innocence" and "the darkness of man’s heart."
For more on the symbolic nature of this novel, visit the attached eNotes link on themes.