After you get the final Sacred Flame to power up your sword, Fi says to go to the Sealed Grounds.
Approach the Gate
Go to the green column and descend to the Sealed Grounds. Go into the Sealed Temple at the Sealed Grounds and approach the Gate of Time. After the cutscene, charge up your sword for a Skyward Strike. The seal on the Imprisoned will fail again. Go outside.
The Imprisoned
After Groose introduces the Groosenator, go down to the very bottom of the Sealed Grounds. When you reach the Sealing Spike, it will fail and The Imprisoned will come out.
Attack the toes. Once all of the toes on a foot are gone, that foot will no longer send out shockwaves when it stomps. You can deflect the shockwaves with Shield Bashes, but it can be difficult to do so.
Eventually it will start climbing the wall. Groose will speak up at this point. Press the indicated button to use the Groosenator, and Groose will explain the controls. Hit the Imprisoned anywhere on its body with a bomb to make it stop climbing the wall. After that, kill its remaining toes. If necessary, use more bombs from the Groosenator to stun the Imprisoned again.
When it falls down, hit the Sealing Spike into its head by slashing your sword upward at the Spike.
If needed, use one of the side air vents to go farther up. (The center air vent will send you all the way to the top and you will have to skydive back down if you use it.)
The Imprisoned will get back up. Hit it with another bomb when the Groosenator is ready. This will make it stop moving temporarily, so kill its toes again, using more bombs from the Groosenator, if necessary, to stun it. Remember that When The Imprisoned falls, hit the spike into its head a second time.
It will glow red and slither up the slope. Use the Groosenator to stop it, then kill the toes and hit the spike into its head a third time. The spike will go back down to the pit, so go down to it and follow the on screen instructions to slash your sword in the proper pattern and seal the spike.
Open the Gate of Time
Make your way to the top, then go into the Sealed Temple and hit the Gate of Time with a Skyward Strike. There will be a cutscene. Afterward, talk to Impa, then go up the stairs and approach the door there. After this cutscene, you can talk to Impa if you wish. Then go back through the Gate. During the cutscene that follows, Groose mentions planting a sapling. Keep this in mind for later.
Find a Pumpkin Patch Plower for Kina
If you go to the Pumpkin Landing, talk to Kina and she will ask you to find someone to plow the pumpkin patch. Tell her that you know someone. Fi will add the pumpkin patch plower to your dowsing targets. Dowsing will point you to the red column of light.
Go to the red column of light and land at the Volcano East statue, and skydive into the structure to the north. Land on the round column to the north. If you miss, go northeast and use the air vent to go back up and try again.
If you landed on the correct column, you will find Guld, the Mogma leader. Tell him you know a place, then ask Fi to summon Scrapper. Then return to the sky. You can't use the nearby Bird Statue to go to the sky, so go northeast to the large air vent to go outside, then go south, then use the westernmost air vent to go up the ledge, and go south to the Bird Statue to return to the sky.
Fly to the Pumpkin Landing and approach Kina. After a cutscene, you will get 5 Gratitude Crystals.
Replace Sparrot's Crystal Ball
Talk to Croo in the dining area of the Bazaar to find out that the Fortune Teller's crystal ball has been broken. Find the Fortune Teller's house in eastern Skyloft. It is the easternmost house, and can be reached by going through the covered walkway north of Gondo's house. Talk to Sparrot and agree to help, and Fi can add the crystal ball as a dowsing target.
The dowsing signal points to the red column. Descend to the Temple Entrance Bird Statue. Look up above the door of the temple to see a crystal ball to the left. There is a Clawshot target on the wall farther to the left. Go west to the air vent that you can reveal by digging in the soft soil, and ride the air vent up to the ledge. Then use the Clawshots on the target. Go east along the ledge above the temple and examine the crystal ball. Ask Fi to summon Scrapper, then jump down and use the Bird Statue to return to the sky.
Go back to Sparrot's house in eastern Skyloft, and after a cutscene, you will get 5 Gratitude Crystals. He will also give you a permanent 50% discount from then on.
Find Clues
In Skyloft, go into the Knight Academy and talk to Headmaster Gaepora in his office on the second floor. He doesn't know where to look, so head for the door. Before you leave, Gaepora says that Levias would know how to find it. Levias is said to be trapped in the Thunderhead. Go into Professor Owlan's office next door to Gaepora's office.
Owlan tests you on the Spiral Charge. Run off of the pier and call your Loftwing. Use the Spiral Charge to break the 10 targets in under 120 seconds. Wait until you are fairly close to each target before using a Spiral Charge.
After you have succeeded, Owlan says to ask the owner of the Lumpy Pumpkin for information about how to approach Levias.
Go to the Lumpy Pumpkin and talk to Pumm. He makes a batch of pumpkin soup in a huge basin to take to Levias. Scrapper will be summoned to carry the basin. The owner says to land on the island with the rainbow.
Summon Levias
Fly to the Thunderhead and land on the island with the rainbow. The possessed Levias will attack.
Run off of the platform and call your Loftwing. Use a Spin Charge to kill all of the eyes on Levias's sides. The flying monsters can be killed with a Spin Charge to their orange tails.
After you have destroyed all of the eyes, fly over the flat part of Levias's head and dive off of your Loftwing to land on the flat part, but don't take out the Sailcloth or you risk going too far and not being able to land. Just skydive onto the flat part, then run to the parasite in the head.
Bilocyte
The eye parasite spits out green spiky things. Slash left and right with your sword to knock the green things into the frills on the sides of Bilocyte's head. Then slash up or down to knock one into Bilocyte's eye. Bilocyte will fall down, so don't let it land on you. Then run over and hit the eye repeatedly with your sword.
After a while, Bilocyte will move to the side after spitting the green things, so you will have to hit the green thing to the correct side. Keep hitting its eye this way until Bilocyte is defeated.
Talk to Levias
Levias will return to normal and tell you about the Song of the Hero. Levias knows one part of the song, and the three dragons know the other parts. Levias tells you to come back to him after you learn the other three parts.
Run off of Levias's head and call your Loftwing. There are several things you can do now that you have helped Levias.
Unlock Bug Heaven
Stritch can now be found on the large southwestern island inside the thunderhead, on the west side. (If not, exit the thunderhead and then go back in.) Talk to him to play the Bug Heaven bug catching game.
Find Beedle's Horned Colossus Beetle
Talk to Beedle in the Airshop during the day and he will ask you to sleep on the bed in the Airshop until night. Do so, and go outside. Talk to him to find out that his Horned Colossus Beetle has gone missing.
Go back to the bed in the Airshop and sleep until morning. Fly into the Thunderhead and talk to Stritch at Bug Heaven (see previous section for more information). He says he found Beedle's beetle, and won't let you have it unless you pass his bug-catching challenge. You need to catch ten insects of Stritch's choosing within 3 minutes.
Once you succeed, Stritch gives you the Horned Colossus Beetle. Be aware that after you give it to Beedle, the next item you purchase from his shop will be half price. If you want to apply this discount to the most expensive item he sells (a Piece of Heart), don't give him the beetle until after you buy the Life Medal. Otherwise, the discount will go to the Life Medal instead, since you have to buy it before Beedle will sell the Piece of Heart.
When you are ready, go to Beedle's Airshop and sleep on the bed in the Airshop until night, then go outside and talk to Beedle and you will get five Gratitude Crystals. Also, as mentioned above, the next item you purchase from his shop will be half price.
Owlan's Plant Request
The next time you talk to Owlan, he will ask you to look for an exotic plant. Fi can add this plant as a dowsing target for you.
Moving On
When you are ready, you can fly to one of the columns of light to learn the dragons' songs for the Song of the Hero quest. You can go to the red column and visit Eldin Volcano to learn the Fire Dragon's Song, you can go to the yellow column and visit Lanayru Desert to learn the Thunder Dragon's Song, and you can go to the green column and visit Faron Woods to learn the Water Dragon's Song.