The darkness of man's heart is central to the novel.
Golding himself has said that the writing of Lord of the Files was "an attempt to trace the defects of society back to the defects of human nature."
In a story of the descent into savagery of a group of young boys, we are provided with an argument regarding the fundamental nature of humans, which includes a great darkness.
The characters of the story begin as innocent beings. They are "just boys" whose response to being stranded is to frolic and play in their accidental freedom. The fact that these "innocent beings" end up as savages, hunting and killing one another demonstrates Golding's notion of what kind of forces exist inside all people.
The descent into savagery is not only thematic to the story's themes. It is central to the plot of the novel as well. Examples relating to the change from relative innocence to real savagery occur often in the second half of the book.
We see in this section of the novel a battle between the strong will of Ralph and Piggy to remain civil and "good" against the animal force of "evil" represented by Ralph and his cohort.
Simon's ritual killing, to which Piggy and Ralph are unwitting yet complicit witnesses, is perhaps the decisive blow in the battle between the forces of good and evil.
Looking at particular characters, Roger is the best example of a boy with instincts toward malice. Instead of relishing the freedom to play on the island, Roger sees an opportunity to be cruel.
He throws stones at Henry to intimidate him, relishing the freedom to be mean.
Killing Piggy with a stone is another example of Roger's darkness of spirit.