When you reach the desert again, talk to Golko right at the entrance and he will tell you he has found the entrance to the Thunder Dragon. Go forward along his ledge and grapple through the canyon to enter the Lanayru Mines. To the south, there will be a hole to crawl through that is blocked by rocks. Roll a bomb through and then get to crawling through to the doorway on the other side and enter the gorge.
Equip the hook beetle and use it to grab a bomb flower from atop the cactus on the right and destroy the rock pile on the pillar that leads over to the locked door. To get the key for the locked door, use the hook beetle and fly past the dragon bones and down into the gorge to find a platform down below with the key resting on it. Pick it up with the beetle and you will receive it. Hop across to the locked door and then hit the crystal in the cart. Now you will need to follow the cart along the tracks as it changes time. At each door, you’ll need to press the blue pressure plate to open the door. At the second door, you’ll need to climb the vines on the right to find it.
Drop down and run through the door and across the blocks that appear. Go left and up the vines to another platform and across to the far side where a baba will appear. Kill it and then grapple to the vines on the other side to find the blue button there. Grapple across the tunnel again and then shimmy to the left, avoiding the wind spouts, until you reach the blocks that appear under you. When you do, hit the next blue button and then you will need to grapple form left to right all the way down the tunnel to the next door. Grapple to the vine at the end and drop down to go through.
Continue following the cart and after a couple of whip jumps over gaps, you will come to a door that has two heart flowers on the right and a lever high up on the wall. Run up the right side of the hill, through the quicksand, picking up the stamina fruit along the way to get to the lever. Pull it down and then quickly drop down and follow the cart into the next room. In here you will need to take down a few Beamos, and then whip the lever that was behind the Beamo to the left of the door.
Once through the door, hop over the blocks that appear and take out the Baba’s. When the cart stops, use the hook beetle to grab a bomb flower to the right of the cart and drop it on the pile of rocks. Continue on, killing the rest of the Baba’s that appear. When you reach the other side, the cart will park and the area will revert time.
Talk to the Thunder Dragon and he will be sick and talk about the tree of life. Make your way over to the bridge to the north east and run across the sand to the tree. Blow the sand out of the way and hit the crystal there. Grab the seedling from the ground and be sure to get the Goddess cube in the corner. Change time back and then return to the bridge, hitting the crystal on the cart with your hook beetle and the entrance area.
Now that you have the seeding, you need to plant it somewhere where it has TIME to grow. Head to the sky and then to the Sealed Ground and enter the Time gate inside the temple. When you are back in time, go the left and plant the tree in the dirt there. Go back through the gate and roll into the now grown tree to get the fruit. Once you have it, head back to the sky and to the Desert Gorge to talk to the Thunder Dragon.
Once you have had your chat with him, go to the sky and back to the Thunderhead. When you enter, look on the map for the position of Levias and fly over to him. Dive off your bird when directly over him and land on his back and he will sing the last part of the song for you. Once he’s done, you’ll need to endure the last trial, so leave the Thunderhead and return to Skyloft. Make your way to the light tower and the entrance to the trial will be to the right of it.
Goddess’s Silent Realm
Now that you are in the silent realm of Skyloft, you need to do the same thing as the previous three trials and collect 15 tears without getting caught or spotted by the phantoms. Thankfully this trial is easier than the rest have been and there is only one tear that should be any trouble at all. At the knight’s academy, there is a tear that you need to move a box under to be able to grab it, but other than that, the rest are a breeze. Once you have collected them all, you will receive the Stone of Time.
Now that you have the stone, you need to place it with the other. If you may have noticed in your travels there is a statue on the island that has one red eye. Make your way to the far Northeast platform by hoping across the three platforms and walk to the statue of the one eyed bird. Once it does its thing, grapple over to the newly formed building and enter.
This area can get a little confusing at first. When you enter, walk up to the table on the left side and it will show a series of blocks in a sliding puzzle. These blocks represent the rooms that you will need to go through to get to the three TriForce pieces. Below are the rooms and the ways to get through each.
Door on the Left and Top
This room will require you to go to the far right side and then use the hook beetle to free the rope on the far side. Once the rope is free, whip to the branch and then jump to the rope and swing over to the far side. Grapple to the vine covered cylinder on the left and wait for it to turn and grapple to the next. When on the second cylinder, grapple to the target and drop down. Now use the hook beetle to grab the bombs on the cylinder and fly them to the fire breathers that are shooting flames towards the ropes. Now swing on the rope and land on the wooden platform. Use the Gust Bellows to swing the platform over to the ledge. Hop off and use the lever to make the room easily accessible next time and go through the door.