The speaker is quietly comforting someone who feels alone in the dark. They begin by admitting that the loneliness is real: "I know it's lonely in the darkness." There's no attempt to brush the feeling aside. Then comes a gentler guess, that nobody has ever said the one thing this person needed to hear. The final line, set apart and indented, delivers it: "You are the moon."
The image turns the darkness around. The moon is only visible because of the night, and it is alone in the sky, yet it is also what people look up at and what gives light when everything else is black. So the person's isolation becomes a sign of how much they matter. The speaker seems to see something in them that they can't see in themselves.
The mood is soft, tender and hushed, which fits the title "Whisper III." It feels like something said close to someone's ear, short and sincere, leaving the last line to linger.