After gathering the 3 shards from around the willow glade, Lungoray will start to invoke the Harmonic from the Song Willow. He gets shot and you have to take over.
Gathering the Harmonic involves planting the shards around the Willow ('Y' button) when you feel the harmonic in your body. You should be circling the Willow at 15-20 feet listening, you'll hear the sound increase as you get closer to each of the harmonic spots and when you're on target (or close enough) the controller will vibrate and you'll be prompted to press 'Y'.
After you do this for all 3 shards you receive the song which you need to take back to the HomeTree and sing.