According to SparkNotes, there are two major conflicts in the "Lord of the Flies" by William Golding: the circumstance of being stranded on an island and the conflict of whether they will set up a civilization with order or descend into savagery, chaos and violence. Golding explored the dark side of this conflict in human nature through these marooned boys and their choices.
The major conflict of civilization versus savagery is embodied by two of the main characters: Jack and Ralph. At the start of the story, the boys elect Ralph to lead them. Ralph comes to represent reason, order and civilization. Meanwhile, Jack is more interested in hunting and finding the beast. He eventually takes over from Ralph and starts his own tribe. Jack leads the boys in violence and blood thirsty hunts. The beast that Jack and his tribe chase is imaginary.
One of the boys, Simon, tries to reveal that the beast is inside them--another conflict and theme that Golding created with innate human evil. Jack and his followers do not accept this news, and they savagely kill Simon and later Piggy. By the time the boys are rescued, they have lost their innocence; savagery has won out in the conflict with civilization.