You will immediately notice that the Desert Colossus is not a friendly place. Any time you are standing on the sand you will be attacked by Leevers. You can stop them from attacking you by standing on any of the stone structures.
The first thing that you should do is to look for a small rock formation just to the north with a crack in it to locate the next Great Fairy’s Fountain:
Travel southward and look for a circle on the mini-map. Make sure that it is night time and you will find a 
Gold Skulltula clinging to one of the palm trees near the pit. Hit it with your 
Longshot and pick up the token (number 92 of 100).
Approach and enter the large Colossus and into the Spirit Temple and then exit the temple as there is nothing that you can do inside the temple just yet. Sheik will drop down from the rocks.
Sheik will tell you that in order to restore the Desert Colossus and enter the Spirit Temple you must travel back to the Spirit Temple as young Link. Sheik will then teach you the Requiem of Spirit.
In order to complete the Spirit Temple, you must travel back to this location as young Link. Use the 
Ocarina of Time and play the Prelude of Light to warp back to the Temple of Time.
Place the 
Master Sword back into the Pedestal of Time. You will need some bugs very shortly so head back to Hyrule Castle and look under the rocks there if you don’t have any on you.
Play the Requiem of Spirit to return to the Desert Colossus. Travel towards the Spirit Temple entrance to find a mound of soft soil out front. Place the Bugs on the soft soil to make a Gold Skulltula appear. Destroy it and pick up the token (number 93 of 100).
Plant some Magic Beans in the soft soil. Note that this should be the last of your 10 Magic Beans – you are all done with the planting aspect of the Magic Bean side quest.
Take this time to travel back to the Desert Colossu and obtain the last Heart Piece:
Ride the Magic Bean Plant at night and hop off as it rotates around the second smaller mountain. There is a Gold Skulltula hanging out at the top – kill it and pick up the token (number 94 of 100).
Head inside the Spirit Temple to begin the final temple dungeon of the game.
