Once you come back, go and speak with the Thunder Dragon again. He’ll munch on the Life Tree Fruit and be completely cured of his illness. As one part of your reward, you’ll learn the third part of the Song of the Hero.
Then you learn of the second part of your reward. By speaking to him after this conversation, you can rebattle bosses you’ve fought throughout the game in a series. The further you go in this series, the better your prize when you quit. I highly recommend doing this – quit when you can get the Piece of Heart and the “Absurdly Sturdy Shield” (it is the IMPOSSIBLE-to-break Hylian Shield). You can also fight all of the bosses in a row for 2,000 or 9,900 (?) Rupees – it will depend on whether it is Hero Mode or not. However, you will seriously want to note that all you can use during these fights are your sword, EQUIPPED shield, and any items you had at the time you originally fought the boss. You also can redo the Silent Realms for other prizes, but the boss fighting has the most prestigious rewards.
Anyhow, do what you want here, then return to the sky.