Theme is the story’s moral or message. Since Lord of the Flies is allegorical, we need to look at what lesson the story is trying to teach us. The main lesson is that without external forces keeping them in line, people are savages.
An allegory is a fairy tale or fable that is written to tell us something about human life. Golding’s tale of a bunch of boys who get stranded on an island and try to form a society but end up killing each other is clearly allegorical. Golding is trying to tell us that human beings are savages at our core. We are more likely to fight each other and look for our own interests than to help each other. The innocent characters who do act morally—Simon and Piggy—are the ones who are killed.
When Ralph is rescued, he thinks back at what has happened and immediately begins crying.
The tears began to flow and sobs shook him. He gave himself up to them now for the first time on the island; great, shuddering spasms of grief that seemed to wrench his whole body. (ch 12)
Ralph’s reaction is a demonstration of the loss of humanity the boys have suffered. When isolated on the island with no adults, they civilization broke down. Ralph is crying not just because of what happened on the island, but because he has learned a terrible fact about human nature.