Once you are done at the Temple of Time, hop on your bird and return to the Sealed Grounds just before the Faron Woods. Talk to the old woman in the temple and she will tell you about the harp and a few other things. When all hell breaks loose, you’ll need to run outside, jump to the bottom of the pit and deal with the Imprisoned. Simply hack at his piggy’s until he falls over and then run to his head and up slash the spike three times. You will need to do this to the Imprisoned 3 times bore he can be defeated. Once he is back in his hole, jump down and strike the spike to drive it back into the ground. Head to the statue after another talk and go back to Skyloft.
Enter the academy and talk to Headmaster Gaepora about the song and he will mention the Light Tower. Head out of the academy and make your way to the windmill that is in front of the Bazaar. Use the Gust Bellows on it to turn it to the position where the shield on it lights up blue. Make your way to the far southeast of the town to talk to Jakamar there about the second windmill. He will tell you there used to be a propeller on it but it fell off. Go to the bazaar now and talk to the scrap dealer and he will regale a tale of his old robot. Give the vendor an ancient flower and the robot will then be under your control. Next up go talk to the fortune teller and he will tell you where the propeller is located.
Since it seems to be near a temple of fire, head to the Eldin Volcano and use the Temple Entrance location. Once you arrive head to the left of the temple and slide down the slope to find it on the ground next to the knocked over tower. Once you have it, head back to Skyloft and to the second windmill. Jakamar will fix the windmill and you can then use the Gust Bellows to turn this windmill just as you did the other. Once the shield on it lights blue, the top of the light tower will extend and that’s your next stop. Head over there and climb to the top. Stand in the light and then play the harp to the timing of the light on the ground. Once all that is over and done with, hop on your bird and make your way for the newly opened hole in the clouds.
Once inside the Thunderhead, drop down to the circular platform across from the tower the light is pointing to. When you land, you will need to line up the bridge pieces using the lever in the center and the three gems that control which blocks will pop up. It’s a rather simple puzzle where you just need to line up the three blocks in a row while moving which blocks pop up out of the ground to stop them from moving. Easiest way I found was to line up all three blocks and then move them all at once, stopping to lower the blocks in the path as necessary. Once the bridge is lined up, run across and crawl through the opening. Make your way down the ramp and hit the symbol with a skyward sword strike to get Farore’s Melody and to learn the next destination.
Enter Faron Woods at the viewing platform statue and then head down to the large circular patch of dirt in front of the structure there. Play the harp and the symbol for the trial gate will appear. Give it a stab and you will enter into Farore’s Silent Realm for your trial. When you start the trial, you will need to wander about and pick up 15 tears without getting caught by the Phantoms in the area. When you grab a tear, the phantoms will remain stationary, but when time runs out on the flower in the top left hand corner, they will come hunting for you.
Once you grab all 15 tears, you still need to make it back to the beginning where you started, so you will definitely want to have at least one tear remaining near the start. Once you have all 15, return to the circle and you will receive the Water Dragon Scales. These will allow you to swim underwater freely. Since you can do that now, head to the body of water near the center of the forest and dive into the cave there and swim through to the Great Tree.
Climb up the vines and then take out the Froaks floating around. Hop over to the wooden platform and use the Gust Bellows to swing back and forth. Hop off the other side and head through the door and you’ll end up outside. Climb the vines and make your way left and up to another entrance. Slice up the shield of the fatty inside and then toss a bomb to remove him. Continue up the path to the top of the tree and you will meet Yerbil after waking him with a slingshot hit.
He will tell you to find the symbol and how to get into the door to meet the water dragon. Go to the red X on your map and talk to Fi when you reach the symbol on the ground. Now make your way back to the pink door at the south of the forest with the similar symbol on it. Walk up to the door and use the Skyward power to draw a circle on it and it will open up for you.
Once you jump off the edge and land in the water, follow the sea creature to the blocked tunnel and then spin through by shaking the nunchuk. Continue following him to the next large room and then use a Froak to blow up the blocked tunnel on the left side to continue on. When you reach the next area, you will need to do a jump over the gated barrier. Dive down and then swim upwards towards the gate and spin as you reach the surface to jump out of the water and over the gate.
You will need to do the same thing in the next room too to get on top of the ledge and reach a save statue and a chest to the right, while you can also go around to the left to find a Goddess Cube. Hop into the next pool of water and follow the tunnel until you run into a large fish with some big lips. Spin into it to take it down and then wait for your friend to open the door to the Water Dragon. After the conversation, head out through the door behind her and you will then need to make your way ALL the way back to the Skyview Temple in the Deep Woods.
Once inside the temple, go to the first large room and go to the right. Swim down in the water and go through the opening on the left side wall. Climb the vines and dig in the opening at the top to find a key. Go back out to the main room and go through the center door. Now you can make your way to the right side of the next room and follow the corridor all the way to the large door where you used the golden key previously. When you enter this time however, instead of there being one skeleton, there will be three of them waiting for you.
Once you take them down, go through the final door to find the sacred spring all the way at the rear of the room where the fairies are flying about. Use your glass bottle to scoop up the water and then head back to the Water Dragon and she will lead you to the flames resting place.