One interpretation of "The Lord of the Flies" is as an allegory of good vs. evil with the island respresenting a type of Eden. On this picturesque island of idyllic climate, replete with fruit and meat, Ralph in the opening chapter removes his clothes and bathes in the water as an act of a baptism, accoring to some critics. This baptism, however, is not sufficient for the removal of sin since the island is a false Eden as there is corruption already within the inhabitants.
The idyllic life of the island is corrupted by the fear of the boys, a fear that they call "the snake thing." This "snake thing" is not like Satan in the Garden of Eden, though, because it is not external; rather, it is the innate evil impulses that the boys possess. So, while Ralph represents the golden boy free of sin, Jack, and especially Roger, represent the evil inherent in man, an evil that without the controls of society dominates.
On the other hand, Simon is the character who is intuitive, spiritual, and much like the prophet who comes to warn of evil. His confrontation with the "beast" who represents the devil is likened to Christ who after 40 days in the wilderness confronts the Devil. After this confrontation, Simon tries to warn the boys, but, like many prophets, he is rejected and even killed by the evil forces of the island.
In the end, the boys are rescued by a savior in the form of the naval officer. But, he, too, is of innate evil as he is from a war-torn society, so the promise of salvation is certainly marred as suggested by the officer's glance to the warship.
The allegory is of the island. It's a micro-society representing a small version of the real world. From the beginning of the book, the reader has to assume that Britain is at war. The plane was escorting a bunch of boys from their private school out of harm's way. Then when it was either shot down as some believe, or even something nuclear killed the engines of the plane causing it to go down, the boys formed their own little society. The themes used in the novel by Golding mirror what society was doing while they were in school. Civilization is in ruins and the only way to really survive is by savage instincts.