After reaching the Temple of Time and being told to go to the Sealed Grounds, use the green column of light to dive down to Faron Woods.
After the cut scene, go into the building. Talk to the old woman to learn how to play the harp. She will teach you the Ballad of the Goddess.
After another cut scene, go through the door behind the gate. Jump down into the pit, using the sailcloth to float down safely.
Destroy all of The Imprisoned's toes. There are three on the front of each foot and one on the back of each foot. Be careful to run away if it's about to stomp.
When it falls over, run over to its head and slash the sword upward to pound the sealing spike into its head.
The Imprisoned will turn red and slither up the slope for a while. You can't hurt it at that point. Just use air vents to float up to the front of it again.
Eventually it will slow down and start walking again, although it gets faster each time you pound the spike into its head. Kill the toes, slash the sword upward to pound the spike in, and repeat the process.
After pounding the spike into its head three times, it will be sealed again. Go down to the bottom of the pit once more and hit the sealing spike with a skyward strike. Then slash your sword as shown in the triangle on the screen to finish sealing The Imprisoned away.
Learn What to do Next
You will learn that you have to find the sacred flames in Faron Woods, Eldin Volcano, and Lanayru Desert in order to strengthen your sword. The clues to the locations of the flames are hidden in the Ballad of the Goddess. You are told to find someone in Skyloft who knows the secret of that song.
Find a Gossip Stone
Go out the way you first came in, to the east. There is a bird statue up ahead. Talk to the Goron, who mentions that you should play a beautiful song where you see butterflies. Strum your harp near the butterflies to make a Gossip Stone appear. The Goron mentions something about Goddess Walls, but doesn't have more information.
Return to Skyloft
Use the bird statue to return to the sky. Fly to Skyloft. Go into the Academy and talk to Zelda's father, Headmaster Gaepora. Ask him to tell you the lyrics of the Ballad of the Goddess:
Oh youth, guided by the servant of the goddess... unite earth and sky, and bring light to the land.
Oh youth, show the two whirling sails the way to the Light Tower... and before you a path shall open, and a heavenly song you shall hear.
The headmaster mentions that the Light Tower is a real place. It's the tower on the end of the island, near where you started the Wing Ceremony.
There are two windmills on Skyloft. One of them has a propeller on it like the kind that you found in the last dungeon that you could activate with the bellows. However, the second windmill's propeller is missing. Kukiel's father is nearby and says that the propeller fell down below the clouds. He says to ask the guy at the Scrap Shop if he has a way to bring the propeller back from down below.
Talk to the guy at the scrap shop. If you don't have an Ancient Flower, go to Lanayru Desert and activate time crystals. Almost any timeshift stone that you activate will have an Ancient Flower somewhere within the time field.
Give the scrap shop guy an Ancient Flower to reactivate the robot. You will now be able to go down below the clouds and dowse for the propeller.