The tone of Lord of the Flies is consistently dark. Parts of the novel are funny: the boyish dialogue, for instance. And it is often emotionally touching to watch the child characters develop. However, the characters being children also makes the tone much darker when, for instance, a character dies or is put in danger. The ever-present reminders of the war in the world outside the island also add to the dark and pessimistic tone.
As the novel progresses, the tone is more consistently dark because of the actual events of the novel, the imagery, and the isolated setting. The pessimism and dark tone come in large part from the preventable nature of the story's progression. There is irony to the events of the story: the boys could have mostly or all survived, and they even could have been rescued sooner. But their adherence to Jack's leadership and natural savagery makes the boys their own worst enemy.
The events of the story are relayed with very little interpolation from the third person narrator. Things are set out as a matter of fact, even when they are unbelievable or the reader might want more information, as when Simon communicates with the pig skull.