Once everything is said and done, it's time to return to the Sealed Grounds. You are advised to restock in Skyloft, get any upgrades you might have available, then head to off.
Right as you're descending, an unexpected visitor... skydives into you. Groose is shocked by this new land, but he quickly regains his ego and goes off to save Zelda on his own. Go into the Sealed Temple to trigger another event. Follow the instructions in the harp tutorial to move on.
After you finish sealing The Imprisoned back into the ground, head back to Skyloft, the Knight Academy to be more specific. You need to talk to Gaepora, who'll be in his office on the top floor.
The thing you have to do now is turn the two windmills in Skyloft towards the Light Tower. One is found to the west of the actual light tower, easy to spot. Use the Gust Bellows to turn it towards the tower. An indicator light will turn on when it's in the right position. If you overshoot you'll have to make a full circle though.
The second tower is east, a bit farther away. Going here you'll see that the propeller from it is gone. Head to the scrap shop in the Bazaar and talk to the shop keeper.
You will now have to give him an Ancient Flower. In your journey through Lanayru Desert you might have picked up some, this guide will assume you didn't. They are flowers that grow all around Lanayru Desert, in timeshifted places where there's grass. You will have to wander around a bit, hitting timeshift stones and keeping an eye out for the flower. Once you have one, return to the Bazaar.
Now it's time to look for the propeller. Go to Eldin Volcano, the Temple Entrance. Go west, down the slope to the broken down tower where a temple key fragment was. Examine the propeller to get it to the sky.
Back in Skyloft, the propeller will get fixed, and you can turn the windmill. Go to the Tower of Light and climb up. Play the harp in the middle to trigger an event. Follow the rhythm as before, and a new path will open.
Once you fly through the portal, continue to the tower to which the light beam points. Once you land you'll have to solve a puzzle. The pillar in the middle is used to rotate the three blocks around their respective paths. The control panel with the three crystals controls which walls are up and which are down, essentially allowing you to re-arrange the relative position of the blocks from each other. They have to be aligned in position in such a way that the actual blocks they correspond to form a bridge to the tower.
In order to do this, start off by rotating the center pillar 7 steps. Go to the control panel with the three crystals, and hit the one on the right side. Rotate the pillar another 6 steps, hit the top crystal, then rotate once more. Finish off by hitting the right crystal again and rotating the center pillar until the bridge is aligned.
Once the bridge is formed, cross over and crawl into the object. Hit the emblem in front of you. Once you obtain the song, go to Faron Woods, and choose the Viewing Platform as your landing destination. Hop down and play your harp in the middle of the dirt circle (Where the butterflies are). Thrust your sword down as instructed to enter the Silent Realm.
As soon as you regain control in the Silent Realm, run forward and get the first tear. The second one is up the stairs, where the bird statue normally is. Drop back down and go right, along the northern side of the woods. Another tear will be right on your path. Go right and climb up the vines for the next one. One is right in the center of that area, surrounded by water which will awaken the guardians. Get to it via the log.
Another one is along your way to the next area, before the small tunnel you crawl through. Follow the path, minding the Watchers. Climb up the tree root and go left, across the rope for the next one. Follow the same root to the opposite end for tear number eight. Jump down towards the soutwest for another one. Number ten is even further south, but be careful of the Watchers once more. Backtrack a bit and go right. Three tears are here in close proximity to each other. The last one is to the far right in the corner. Complete the full circle around the area back to the starting position to finish the trial.