Get inside the cave, stand in front of the stele and play the Wind God's Aria along with Makar. The door will then open and you can enter the temple.
To begin with, carry Makar and open the door. Play the Command Melody to take control of him, then make him go down and towards a heap of soil. As Makar, plant a seed to make a tree grow, do the same with another heap of soil, then fly north and jump on the switch. Take back control, open the chest down there to get 100 rupees and drop a bomb north to clear the way to the warp pot. Go back to the spring, get on it, look at the entrance, put on the Iron Boots, take them off and jump towards the entrance. Then, get on the spring up there, put on your Iron Boots, take them off and quickly take out your Deku Leaf to hover to Makar. Carry him and open the next door.
Get rid of the Armos, then swing your Deku Leaf to switch on the leafy pinwheel and rotate the iron gate. Take control of Makar, make him go ahead and plant two seeds in the heap of soil, then open the door with him. Once more, take control of him, make him fly on the platform to the right, plant a seed, and so on until the third seed. At this moment, the doors will unlock, but he will get caught right under your nose! Open the door to your right.
You will see Makar locked up north of the room. Go east and open the door. Jump down, get rid of the Wallmaster and switch on the pinwheel to lift up the gate. Then, clear out the other Wallmaster and activate the pinwheel again to lower the gate. Use the spring to reach the upper level, find a Joy Pendant in the chest north, then open the south-east door.
Here, fly with the Deku Leaf towards the whirlpool, then head towards the eastern corner. Walk on the switch, then fly towards the lowered gate to the right. Walk on the iron gate, jump right and get rid of the Wizzrobes using some arrows. Then fly south to the chest containing the Map, then fly, or walk and use the vines, back to the entrance. Fly once again in the whirlpool, then towards the gate, then the next whirlpool, fly through the opening in the next gate, go to the next whirlpool and the right gate. Finally fly towards the last whirlpool to reach the west side of this big room (the Wizzrobes should not be a problem) and open the door.
Walk on the spring with the Iron Boots to make the ground gate disappear and clear the way to the warp pot. Get close to the edge and look left. Use the Deku Leaf and fly towards the left gates, then down towards the ledge with a chest and two pots. Pick up the Compass from the chest, then jump all the way down.
Get in the room to the south. Stand on one of the slabs with the Iron Boots to fall on the underground level and get rid of the enemies. Move the block with the spring to the south of the room, on a slab with a drawing on it. Then push a classic block near the spring, climb on it and jump on the spring to get back up. Pick up the Small Key from the chest, then break another slab, get back on, and so on until all slabs are broken to make a chest appear, containing a Treasure Chart. Get out and unlock the door leading north.
Be ready to fight another group of enemies that are quite strong, including Wizzrobes and Darknuts (iron warriors). Try to get rid first of the orange Wizzrobes that can summon more enemies. After this difficult fight, open the chest and pick up the Hookshot! Shoot it at the target north to climb on a platform, hammer down the spike and get out.
Shoot the Hookshot at the targets to climb back about half the height of the room. Then, use the Deku Leaf to hover to the other side (and open the chest if you missed it earlier). Jump on the spring and equip your Deku Leaf to reach the next platform, then go back up with the Hookshot towards Makar. Put on your Iron Boots and shoot the Hookshot at the target on the statue to make it fall. Therefore, your partner will be free and you can get another Joy Pendant. Leave Makar for a moment and jump on the gate right under you, go forward to the other side and shoot the Hookshot at the west target. Take control of Makar and make him get back to you. Open the door with him.
Get rid of the Wizzrobes, then following Makar's advice, cling on the trees using the Hookshot. Then take control of Makar so he can join you and open the door. Little by little, make your partner fly towards a platform, plant a seed, then shoot the Hookshot to go up. Clear out one or more skulls with the combo Hookshot/sword and repeat until you reach the top of the room. Open the door. Place Makar on a switch and stand on the remaining one to open the gate in front of you, along with another one located in the underground.
Get close to the edge and look down to the left (where you already went). Fly towards this place and get rid of the two Armos with bombs. Then play the Command Melody and make Makar fly to you. Carry him and open the door. Leave him next to the door and fight the enemies. Then, jump, put the gate in a horizontal stance, go forward, put the gate back on a vertical stance and jump using the spring to get back up. Switch on another pinwheel to lower the gate again and go to the stele with the notes engraved on it. Take control of Makar and make him go all the way to you. Play the Wind God's Aria to break the stele and open the door
Here you will have to get rid of three Darknuts. As usual, you will have to cut the ropes on their back and then attack them from the front (the spin attack or the cyclone attack can be useful). Pick up the Big Key, then get back into the circular room with Makar (simply switch the pinwheel to cross the gate). Next, carry your friend and jump all the way down to the basement. (If you fall under the propellers, walk on the switch to get back up.)
As Makar, plant two seeds in the western heaps of soil to create a whirlpool. As Link (alone), get into the whirlpool with the Deku Leaf and upon reaching the third floor, fly south. Open the door and get rid of the Armos (shoot an arrow to stun them, then break the red crystal on their back). Pick up the Small Key from the chest, then get out and go back down to the underground level. Before this, you can fly east to pick up a Joy Pendant from a chest.
Take Makar on your shoulders, then when the whirlpool stops, walk under the propellers and unlock the door leading east. Once more, be ready for a tough fight, but you can also use the Hookshot straight away to pull yourself at the top of the room. To do so, aim at the target to the south, then at a target to the east and at the remaining targets until reaching the west side. There, walk on the switch with the Iron Boots to unlock the door. However, if you get rid of all the enemies (including those hiding behind the statues), you will be rewarded with another Treasure Chart. Pick up Makar and open the door to the east.
Fight the first enemies, then take control of your partner, make him fly to the other side of the room and plant another seed in the soil. Use the Hookshot to reach the tree, then carry Makar and open the next door. Here, push the block on the right so it blocks the first and second traps on the left. Then, push the second block all the way to the right, then forward until it goes past the first block (put on your Iron Boots when it becomes necessary), pull it two or three times left, then again forward into the gap. Now push the third block, making it go above the second one, so it blocks the third trap. Then go for Makar, carry him to the other side of the room, walk down the stairs, then play the Wind God's Aria and open the door. Clear the way to the warp pot, shatter the pots to catch one or several small fairies and open the boss door.
Get in the middle of the sand room to make the boss appear. In order to beat it, use the L lock to aim at its tongue and shoot your Hookshot at it, while staying far enough not to get swallowed! Upon drawing its tongue at you, quickly hit it with your sword. Molgera will rise above the ground then dive back into it, and you will just have to follow those steps again. Soon it will call for snakes to help it. Hit them with your Hookshot to destroy them and get a heart instead, but keep on striking the boss whenever you can. After getting out of the ground three times, he will be finally down. Pick up the Heart Container, then Makar will get into the room. The Master Sword will get back its full powers and Makar, as the new Sage of Wind, will remain in the temple to pray the gods.