He sees and hears the same thing Samneric see. The difference is that he understands the significance of what he's seeing. The twins hear a plopping and see a flapping but aren't equipped with the maturity to understand what they're seeing. Simon is symbolic of the soul or spirit, and he sees with more mature eyes. Not only that, he releases (frees) the dead parachutist, then tries to explain to the others that the only beast is the one within them--the one which causes them to kill him as he delivers his message.
After Simon encounters the pig's head in Chapter 8 of Lord of the Flies, and he experiences the darkness of man's heart, "what was real seemed illusive and without definition." The Lord of the Flies hangs on his stick and grins before Simon looks back, "his gaze held by that ancient, inescapable recognition."
Then, in a symbolic incident, Simon sees "a humped thing suddenly sit up...and look down at him." Golding writes that "the flies had found the figure,too." Thus, like the pig's head, the decaying pilot, a figure of war, also represents the evil in man. Sickened, Simon, nevertheless, frees the body "that should be rotting away" from the ropes and layers of rubber and canvas. As he prepares to leave, Simon turns to the "poor broken thing that sat stinking by his side"--the symbol of man in a society without civility. Like Moses who returns from the mountain, Simon encounters chaos when he arrives in camp.
This is at the start of Chapter 9. What Simon finds is the dead body of that pilot who had been shot down in the battle back in Chapter 6.
Simon heads down the mountain to tell what he has found -- that it wasn't really the beast. But the boys kill him when he gets down because they are all wild from doing their pig killing dance.