How is the loss of innocence presented in Lord of the Flies?

The loss of innocence is presented gradually over the course of the novel but it does start to snowball towards the end. At first, the boys cooperate with relative success. Ralph is continually frustrated with the inattention to the shelters and the fire, but there is general cooperation at the start. Over time, Jack becomes more interested in hunting, thus tapping into his urge to be more visceral and savage. He becomes more tyrannical in dealing with the other boys and he uses fear to sway them to his own tribe. As more boys flock to Jack's tribe, the loss of innocence becomes more complete. When Ralph is finally left by himself, the innocence is completely gone. All the boys are on Jack's side and this symbolizes their complete conversion from a once civilized island of boys to a group of savages. 

The two pivotal and symbolic events that facilitate this loss of innocence and Jack's triumph are the deaths of Simon and Piggy. Simon symbolizes peace and understanding. In Chapter 9, Simon discovers that there is no real "beast." He goes to tell the others. In their savage frenzy of a ritual, they mistake him for the beast and kill him. They kill the one who had come to tell them that there is nothing to fear. This is extremely significant because the fear of the beast is in the minds of the boys. They would have had to face the fact that the beast was simply a potential in themselves. With Simon's wisdom, they might have dealt with this. 

When Piggy dies, reason dies. With his death, the conch is also destroyed. The symbol and the tool for civilized reason and organization are destroyed. With Piggy's death at the end of Chapter 11, innocence is completely gone.