Go back at sea with Medli and head for Headstone Island. On the island, go back in front of the stele and play the Earth God's Lyric. Medli will play as well and the door will open.
Carry Medli and run towards the door, she will fly while still having a grip on you. Still carrying Medli on your shoulders, open the door.
Note: You must carry Medli while going through a door, or else she will stay behind.
Get rid of the enemies, climb the stairs, then lift Medli and go towards the pillar with the switch to fly with her. Stand on the switch, then play the Command Melody to take control of Medli and make her fly towards the switch on the other pillar. As soon as she stands on the second switch, the door will unlock. Make her go down, then take back control and go through the door with her.
Fight the enemies, draw the dark blue Chuchus into the light, then smash them with your Skull Hammer. Take control of Medli and use her harp to redirect the light coming down from the ceiling towards the transparent chest. Pick up the Map from the chest, then place a bomb next to the warp pot to clear the way to it. You also can shoot a Fire Arrow at the curtain by the vase and use the Boomerang to retrieve the Joy Pendant. Open the next door. Here the purple fog will prevent you from using any of your weapons upon touching it. Take control of Medli and make her point her harp at the stake in the fog right of the statue. Then, go back to yourself and hammer down the stake with Medli still lighting it. Open the south door.
Get rid of the two skulls, first by using the Deku Leaf, then by swinging your sword, then climb the ladder and pull the block to let the light go through. As Medli, reflect the light towards the transparent chest. As Link, pick up the Small Key from the chest and go back to the previous room. If Medli got caught, control her and fly to cross the barriers of the balcony.
Unlock the door using the Small Key. Shoot a Fire Arrow at the curtain on the west side to get some light, draw at least two dark blue Chuchus into the light, and clear out the other enemies. Then place the two frozen Chuchus on the two switches, carry Medli and quickly climb the stairs. Push the block down and open the next door.
Be careful with the Wallmaster here (or get rid of it), then push the block against the wall to get some light. As Medli, aim your harp at the two bottom right and left yellow symbols, then again at the statue on the block to destroy it. As Link, push the block that was holding the statue to make a chest appear. Pull the north block until it reaches the end of the track, then throw Medli towards this block. Climb on it, pick up the Compass from the chest and open the door.
Start by getting rid of the Moblins and the Poes (destroy their lantern first). Then take control of Medli, make her fly to the top of the ladder and make her aim her harp at the three statues to destroy them. Make her go down, then as Link, pick up the Joy Pendant from the chest, climb the stairs with Medli and open the door to the south-east.
Get close to the coffins down there, pick up the Small Key from one of them and get rid of the enemies hidden in the others. Climb the ladder, get out and unlock another door. Now you will have to fight with a Stalfos, swing your sword at it, then when it's down to a pile of bones, quickly smash its skull with your Hammer before it gets back on its feet. Two other Stalfos will appear, use the same method to clear them out, then pick up the Mirror Shield from the chest. Walk into the light, raise your sword (or another weapon), then raise your Mirror Shield to reflect the light at the moon symbol above the door.
Leave the room, fight the enemies again, then play the Command Melody and make Medli fly again to the top of the ladder. Use her harp to reflect the light towards the centre of the room, then go back as Link. Stand into the light and using your Mirror Shield, reflect the light towards the yellow symbol to the west. Go pick up Medli and follow the path. In this passage, you can light up another yellow symbol with the help of your partner to earn 80 rupees.
Back in the room with the huge statue, carry Medli and fly with her to get past the purple fog. Take her control, reflect the light towards one of the statue's eyes, then as Link, do the same towards the remaining eye. Stairs leading underground will appear. Before going any further, you can get back to the room to the south, place Medli on the switch, then enter the next room and use the Mirror Shield on the symbols to get another Joy Pendant from the chest.
Now get down the stairs, open the door and go down some more. Get rid of another two skulls, go across the bridge with Medli and play the Earth God's Lyric in front of the door. Upon Medli doing the same, the door will now be accessible. Open it, fight the two Gibdos, then use your Mirror Shield on the statue in front of you, along with the two mirrors right and left to destroy the two remaining statues.
Leave Medli in this room and open the door west. Go down the stairs, go across the room avoiding the Wallmasters and pick up the Small Key from the chest at the back. Get rid of the Wallmasters to unveil a chest containing a Treasure Chart and go back to the previous room. Now open the door leading east, go across the room still avoiding the Wallmasters, smash down the stake with your Skull Hammer and pull the block holding the great mirror into the light. You can also shoot a Fire Arrow at the curtain on the right to get a Joy Pendant. Go back to the previous room.
Push the block against the wall, throw Medli towards this block, climb and unlock the door. Clear out the enemies (this time you can get rid of the Poes using your Mirror Shield), then take control of your partner and aim the light at the ground south. Take back control and aim the light at the statue to the west, then open the door. Go right, fight the enemies emerging from the coffins and play the Earth God's Lyric in front of the door with Medli. Open the door, go right and use a bomb to clear the way to the warp pot. Carry Medli, go down two flights of stairs and open the door. Note that Link can climb back using the vines if he ever falls down.
Play the Command Melody, make your partner fly towards the platform in front of you, place her on the switch to get some light, then make her go all the way down. As Link, climb down the ladder and pull the mirror into the light. As Medli, fly towards the other platform north-east, aim the light at the transparent chest, then at the statue in the middle of the room and at the pedestal to the east. As Link, open the chest to get 50 rupees and pull the statue up to the end of the track. Then get on the pedestal lighted by Medli, aim the light at the four yellow symbols, then pull the newly-found mirror up to the end of the track. Now go to the south-west corner of the room and pull the mirror. Climb on the western platform and raise your Mirror Shield to light the chest, then the yellow symbol to the south-west and the statue in the middle of the room. Pick up the Joy Pendant from the chest and pull the statue up to the end of its track. Take control of Medli, have her fly towards the platform where you were and aim her harp at the pedestal nearby. Take back control, stand on the pedestal and reflect the light at the four symbols to the north-west. Pull the mirror up to the end of the track so everything is finally set up. Bring Medli on the north-east platform and have her reflect the light towards the right eye of the sun, then go on the north-west platform and light the other eye. The whole room will now be lighted. Leave your partner in this room and open the door to the north.
Get rid of the two skulls, then fight the Darknut by shattering its armour. Pick up the Big Key from the chest and backtrack. If you want to, you can open the door west, light up the coffins, jump and fight the three Stalfos, pull the block against the wall to climb on it and pick up the Treasure Chart from the chest. Once back in the big room, make Medli fly towards the entrance door, climb the ladder and get out with her. Climb the first staircase and make Medli fly towards the second one, while you climb the vines to reach it. Climb the second staircase. Facing the boss' door, carry Medli and fly with her in this direction. Finally, open the door.
This huge boss is made of a dozen of smaller ghosts. Stand into one of the light beams and reflect the light at the boss until he falls down. At this moment, carry him and throw him at one of the spiked pillars. Then run to the small ghosts and hit two or three of them twice. Then the boss will re-form and you will have to start again until all the ghosts are defeated. Sometimes Jalhalla will blow in your direction to push you on the spikes. When he turns pink and jumps at you, the controls will be inverted, so do your best to flee or to reach a light beam. Upon beating him, pick up the Heart Container. The Master Sword will get back part of its mythical powers and you will say goodbye to Medli, the new Sage of Earth.