The previous two posts are, indeed, viable and strong. However, with his ironic ending of the battleship and its officer arriving to rescue the boys who have sought shelter and solace on the island, there is yet another point that can be made with Golding's powerful message in Lord of the Flies. For, coming in the wake of World War II, Golding's novel that was published in 1954 seems to raise the question of whether there is any civilization that is truly civilized as the military officer glances back at the warship from which he has come. If this warship is, indeed, the deus ex machina that arrives to save the boys from their beasts within, what, then, is Golding telling the reader about civilized man?
"The evil that men do" is not merely from stressful situations or in the absence of society--evil is an intrinsic human condition as man has engage in wars throughout history, for the Rogers of the world have their throwing arms only "conditioned by society"; they are always and intrinsically sadistic.
To add to auntlori's answer, we can also consider the novel from a Freudian perspective. Sigmund Freud, a psychoanalyst in the early 1900s, identified and labeled three layers of the human psyche:
- The id is the layer concerned with basic, primal needs. In essence, the id is concerned with the satisfaction of hunger (and the fulfillment of other human needs) and is relatively unrestricted in its drive to attain these. Babies, for example, are driven by the id.
- The ego is the layer of the personality that's driven by laws of society. The ego is developed as a child learns right from wrong (by learning consequences of "bad" behavior).
- The super-ego can be described as a person's conscience, as it develops once a person learns why what's right is right and what's wrong is wrong.
In a psychologically well-balanced person, the ego serves as a balance between the id and super-ego.
In Lord of the Flies, since the children find themselves in a very stressful situation, the boys' ids become increasingly dominant. Because the boys' behavior becomes increasingly savage (what starts as hunting for food turns into hunting for the "thrill of the kill"), we can say that the boys' psyche has become unbalanced--and that the "dark side" of humans is what comes out as a result of the stress of the situation. According to Freud, humans are born with an id that dictates their behavior; William Golding, in writing Lord of the Flies, seems to be making the point that the id is the "dark side" in all of us and will emerge when the laws and rules of society are taken away.
I'm assuming your question is more like what role does the dark side of human nature play in the destruction of society in the novel Lord of the Flies. The simplest answer is that it's this darker side of human nature which leads directly to all the death and destruction in the novel. This is a highly symbolic work, and it's hard to escape Golding's point that a world without any external controls (in this case, no adults and no real laws or restrictions) leads to destruction because the inherent sin or evil in our nature will override any other elements.
Each of the boys represents part of who we are. Piggy is indicative of our intellectual selves, and when he wants to establish some order on the island, he is mocked and ridiculed and ignored--and eventually killed. Simon represents the conscience or the soul of man, and he speaks the truth (that the beast is them) but is not heard or believed; instead, he is also killed. That leaves Ralph, who is symbolic of our physical selves, and Jack, who represents our inherent sin/evil/dark nature. They are the last two elements to survive, and one is nearly destroyed by the other. In the end, Ralph is no longer the leader, he is the hunted. The dark side of ourselves (represented primarily by Jack) is the most powerful part of who we are, says Golding.
Thematically, then, the message is clear--the strongest element in our beings, according to Golding, is that dark side inside us all; and without the restraints and controls of a civilized world, that is the dominant force, though it will inevitably lead to destruction. That's exactly what happens on this island--until the miraculous and ironic rescue at the end. It is the dark side of human nature which destroys this microcosmic world.