Back in the sky, I recommend you first hunt down and open the chests activated by the six Goddess Cubes you struck in recent times. The locations are on the map, by the way, but here is a quick listing anyways.
Treasure Chest 1
The first one you struck is on an island northeast of Skyloft and also northwest of Beedle’s Island, on an upper plateau. It contains a Silver Rupee.
Treasure Chest 2
The second chest is to the southwest of Skyloft, in the vicinity of Fun Fun Island. It contains a Small Seed Satchel.
Treasure Chest 3
The third chest is located in the Inside the Thunderhead on the Isle of Songs. You’ll be initially unable to go there, so note the location of this Gold Rupee for later.
Treasure Chest 4
The fourth chest, also containing a Gold Rupee, is north of Skyloft, behind the main facility of Bamboo Island.
Treasure Chest 5
The fifth chest is found to the northeast of Skyloft, rather near Beedle’s Island, on a small island. It is in an alcove; you’ll need to do some vine climbing to reach this Treasure Medal.
Treasure Chest 6
The sixth chest is actually found in Skyloft. However, it is inaccessible for the moment, so note this for the future. Once you obtain the Water Dragon’s Scale, go into the eastern river and through the hole beneath Kukiel’s house. Swim up to find the room with Heart Piece 4.
Afterwards, head back to Skyloft.
Back home, dive off near the Statue of the Goddess and go through the doorway at the base. In this room, insert the Amber Tablet into the altar to create a electric yellow beam of light, rising from the surface below to indicate the hot and dry Lanayru Desert.
If you have a moment, return to Faron Woods and descend to the “In the Woods” Bird Statue. Turn around so you face the path on the floor. Then follow it right. Watch out for the Deku Babas and stronger Quadro Babas. After a while, you should spot a part of the wall that your Bombs would love to blow up. Do so to find Heart Piece 16.
Anyhow, finish up any other business you deem necessary, then return to the skies on your Loftwing. Go to and drop into the yellow beam of light to the southwest.