The true nature of the beast is only hinted at until Simon begins to unravel the mystery. From very early in the story he suspects that there is something going on but when he wanders off into the forest alone and finds the pig's head impaled on a stick and, in the heat and his exhaustion, collapses and has a vision. In this vision, the true nature of the "beast" is revealed as the so-called Lord of the Flies (the pig's head) speaks to Simon and tells him that the beast is really inside of them and that you can't kill it, the thing they are most afraid of is their own capacity for violence.
This ties together the symbol of loss of innocence represented by the beast from the air and the beast from the water. The first death on the island isn't accompanied by a body and isn't acknowledged by the boys so they still have a sort of innocence intact. Then the body of the pilot attached to the parachute comes down and terrifies the boys but it brings death with it. Because once Simon investigates and finds out what it is, he races down to tell the boys.
But the loss of innocence is complete when he emerges from the jungle and the boys kill him in a frenzy. The boys believe it was the beast coming for them and they kill it, only after do they realize they've killed Simon and their descent into savagery accelerates.