From the moment Zeus is referred to as the god of flies and death, The Flies is full of mood. A mood of guilt, repentance, remorse, and fear, yes, but moreso a mood of sickness, rottenness, tragedy, and doom. The people live their lives in fear and guilt--but that does not make their lives empty. It makes them doomed. The set contributes to the sweltering sense of doom: Act I features a statue of Zeus, Act II, scene i features a giant boulder that holds the dead back, Act II, scene ii features a different statue of Zeus, and Act III features a statue of Apollo. Perhaps with some more time I'll analyze the meaning of the shift in dominant set.
And within this mood of doom, in which the oppressive flies take on an identity of meaning to themselves, Sartre explores his big themes: God, man, freedom, fear, and the Cosmos.