If you want to hunt for the final Goddess Cube chest, you’ll need to go Inside the Thunderhead, north of Bug Rock. Land on the southern end of the island and burrow inside, exiting to the northwest, to find your Small Quiver.
Anyhow, our next goal is to find a place where we can plant the Life Tree Seedling. How about the Faron Woods?
Go there and land in the Sealed Grounds area, then head into the Temple.
Sealed Temple/Temple of Hylia
Head towards the Bird Statue, in the grassy, sunny area. Speak with Groose to note the patch of dirt here. But yet, let’s not plant the Life Tree Seedling there – it would take years and years to grow. Go through the Gate of Time.
Back in the past, speak with Impa if you want to. Head to the past version of the dirt patch Groose mentioned and plant the Life Tree Seedling there. Then go back … to the future! (Getting sick of that yet?)
Back in Link’s time, go to the large tree. It is in the patch of dirt we planted moments/centuries ago. Roll into the tree to get a Life Tree Fruit, which Link himself cannot utilize. However, I’m quite sure the Thunder Dragon can. Leave the temple and return to the sky. Return to the Lanayru Desert and land at the gorge.
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.
Heart Piece 24
I highly recommend doing this – quit when you can get Heart Piece 24 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.
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.