Lord of the Flies is a microcosm for the world at war. It focuses on how the boys, who on arrival pull up their socks with "an automatic gesture," are completely "conditioned" by the society that they live in and moulded by the rules of community. At the start of their time on the island, they stick to civilisation, enforcing rules, such as only being able to speak when you are holding the conch, and concentrating heavily on keeping the fire alight for a successful rescue. This mentality, however, deteriorates as their time on the island progresses. They lose the dedication to rescue and their natural savage instincts are unearthed.
The main character behind this deterioration into savagery and the loss of the boys' innocence is Jack. He paints his face with a mask that "liberates him from self consciousness". With the removal of his uniform, the "knife belt" around his waist and a mask that allows him to behave as someone else and not worry about the consequences, Jack is able to act in an animal like manner. With his tribe of boys, he hunts all day and puts fear into the hearts of the other boys. He creates the concept of the "beast" or "snake thing" on the island that causes the younger boys to become terrified and turn to Jack and his hunting for protection.
This element of fear is crucial in the novel, as it causes the boys to act completely out of character and therefore lose their innocence. They become so scared of the beast that they are willing to do anything to feel safe. This includes killing and hunting. For example, the death of Simon; Simon is a truly good character in the novel and has the most knowledge out of all of the boys. He is aware that the irrational fear of the beast is causing the boys to act dangerously and that the only thing they should actually be fearing is themselves, as they have developed the capacity to kill. However, when Simon runs to try and tell they boys what he knows, he is confronted by a tribal dance, led by Jack, chanting about the destruction of the beast. The boys, in hysteria and in fear, mistake Simon for the beast and brutally murder him.
The lack of adults on the island is also a crucial aspect in the loss of innocence of the boys, as it means that they are in charge. There is no one to enforce rules from home or order them around. This causes them to take things into their own hands and have to cope on their own. This does not go well, as Ralph is a weak leader who does not count out the presence of a beast and does not control Jack. This means that the fear is able to grow and Jack is able to step in and snatch power.
Overall, the loss of innocence in Lord of the Flies is down to the fact that the boys are isolated away from adults and away from law and order. When they are on their own their natural instincts, savage instincts shine through and, spurred on by the fear of the beast and Jack's hunting, the boys begin to kill and feel no remorse. Piggy and Simon both die and Ralph is hunted at the end. Golding is saying here that as soon as social restraints are removed, humans will resort to animal behaviour, like in a war for example. Normal people with normal roles and normal jobs end up killing people. They behave savagely. The boys discover this on the island and lose the naivety and innocence that they arrived with. They witness things that young boys are not meant to, and are therefore initiated into adulthood or at least savagery.