This part will get you through the entire Wind Temple.
With Makar on board the King of Red Lions, let's get underway. Warp to Windfall Island and sail north to Gale Isle. Once you reach the Island, the King of Red Lions will tell Link that if he needs Makar to do something, use the Command Melody to control him. Upon entering, play the Wind God's Aria before the giant stone tablet. Makar will enthusiastically play his violin, and the giant stone tablet will crack and crumble, opening the way to the Wind Temple. The both of them will automatically drop down the hole in the next room and enter.
Inside the Wind Temple
Like with Medli, we're going to need to carry Makar with us through the doors of most of the rooms since he will just stay in whatever room we left him in. In the first room that we enter, head straight to the door, then leap down the ledge to take out the Wizzrobe using Fire or Ice Arrows. Go forward past the two patches of ground with holes in them, defeat the Stalfos, and use a Bomb to blow open a teleportation pot that's nearby. Use the Command Melody to take control of Makar so he can fly down to join us. As with Medli, pressing the A button repeatedly causes Makar to fly for a short while until he sets down to rest or gets hit by an enemy. However, Makar cannot carry us if we leap off ledges with him. Anyway, with Makar down there with us, have him walk up to two patches of ground with holes in them, then press A button when the green action button icon flashes to plant a seed, which will automatically sprout into a vine. When both vines have sprouted, a chest will appear containing 100 rupees.
Next, have Makar fly up to the ledge on the other side of the room to activate a floor button to shut off two downdrafts blowing in the center. With them shut off, have Link climb onto a springboard, then use the Iron Boots to make the spring go down before taking them off to launch Link into the air so he can go back onto the first ledge. While facing the other ledge, use the same method with the springboard on the ledge to launch Link so that he can glide to the other ledge by using the Deku Leaf. Pick up Makar and take him with him through the door into the next room. Take down the two small Armos statues there, then use the Deku Leaf to blow the propeller so that the panel before you can rotate, allowing you and Makar to cross over to the other side where there's a door with metal bars on it. Control Makar so he can plant some seeds near the door to grow vines so the bars will be raised on the door, then pick him up and take him through it.
In the next room there are some ledges that have patches of ground for planting, so let Makar do the flying to the ledges to do some vine-planting. This will remove bars on both the room's doors, but this will also make Floor Masters appear around the last vine Makar plants. They will snatch him away and place him in a prison that he won't be able to get out of yet, so we're going to have to proceed alone for a while. Go through the door on your right, and in the large center room we'll hear Makar's cry for help, but we can't do anything for him right now. Instead, proceed to the door where the two big Armos statues are and blow them up with Bombs. Go through that door, and here we have a room with a bladed trap going back and forth, a panel that needs to be rotated, and some Peahats flying around. Get past the bladed trap and fall down to a floor where there's a single Floor Master to destroy. Use your Deku Leaf to blow wind into a propeller down there to rotate the panel blocking our way to whatever's on the other side of it, then springboard your way back up and cross over on the panel to the other side of the room where you'll see a giant stone tablet that looks similar to the one outside of the Wind Temple, but we need to have Makar to remove it first. So exit through the door on your right.
You'll now enter a large chamber where there's an updraft you can use for gliding your way onto a ledge on your left. Step on the floor button there, and it will open a gate through the grating up ahead. Glide your way onto the gate, then leap over to the ledge on your left and take out the Wizzrobe that will harass you. Glide into the updraft in the center and then fly through the grating on your left to the ledge behind it. On the ledge is a treasure chest that contains the Dungeon Map. Glide back toward the updraft and this time go through the grating that was on your right. You'll come across another updraft that will lift you high enough to get onto the gate of another grating past it. From there, take down the Wizzrobe and the Peahats, then glide into the updraft to take you to the next ledge where there's a door to your right. Replenish your magic before proceeding.
You'll now be in the large center room you were in earlier where you saw Makar imprisoned. From where you are now, push the peg into the ground by wearing your Iron Boots. This will open up the floor, revealing that the room is a chamber that extends down to the basement. Near the door is another teleportation pot we need to open. After that is done, drift down all the way to the basement, knowing that you can conserve magic by dropping and drifting with the Deku Leaf.
Once you reach bottom, go through the unlocked door. The room that you're in has a ledge that's lined with spikes, so we can't climb up to it. Instead, we're going to have to drop down through one of five tiles that we can smash through by wearing the Iron Boots and then arrange some blocks, one of which has a springboard on it, so we can pop up through the hole on the ledge. Depending on which board you smash, you may or may not encounter enemies. When you're on the ledge, open the treasure chest there to get a small key. This will disarm the spikes near the ledge so you can get back to the exit faster.
Open the locked door and enter the room where you'll get into a closed-door battle with a high-level Wizzrobe that will summon all types of enemies, even other Wizzrobes! He will start off by summoning a Darknut and another Wizzrobe into the room. Defeat all the lesser enemies quickly, then move to the center of the room and get the Fire Arrows ready. The high-level Wizzrobe will mostly stick to the ledges above the floor, so scan the room, lock onto him quickly, and fire an arrow at him before he has the chance to summon more enemies. It won't take more than three Fire Arrows to fell him. When the battle is over, a treasure chest will appear that will give us our next useful item -- the Hookshot. As with the Grappling Hook, point the red marker at where you want to aim it at until it turns yellow, then fire. It will pull you over to certain targets, and it can pull other objects towards you.
The metal bars on the door you entered through will be raised up, so go back into the chamber. We're going to Hookshot our way up some ledges to get to the first floor, so get it out and start targeting some spots to pull yourself toward. Go up three ledges to the right and one ledge to the left. Then glide your way across the chamber until you're on the ledge straight ahead of you. Open the treasure chest there to get the Compass. Get up on the springboard and launch yourself up to a ledge on your right. Hookshot up one ledge to the left, then two ledges to the right, then springboard up to the ledge to the right. Go all the way to the right of that ledge, then Hookshot up to where Makar is held prisoner. Put on your Iron Boots and Hookshot onto the spot of the giant headstone to pull it down, thus freeing Makar. Go inside and open the treasure chest to get a Joy Pendant.
Now that we have Makar back, take control of him so that he will drop down to the basement and plant some seeds for creating vines. This will cause a large updraft to appear in the center of the chamber which will turn itself on and off alternately. While the updraft is present, have Makar fly into the updraft so he can be lifted as high as the second floor. Fly Link during the updraft to the door that has four pillars near it on that floor and enter.
This room has a closed-door battle with a group of small Armos statues that need to be hit in their jeweled behinds to make them explode. This will open up a panel that a treasure chest containing a small key is hiding behind. Go out the same way you came in and leap to your right to glide down to the first floor where the big Armos statues are. Have Makar join you there so you can get to the other end of the next room where the big stone tablet is to play the Wind God's Aria. Makar will enthusiastically play the violin to make the stone tablet crack and crumble, revealing a door behind it.
With the stone tablet out of our way, go through the door with Makar and you'll have a closed-door battle with some Darknuts. Defeat them and a panel will open up leading you to a treasure chest that contains the Big Key. Head back out the same door and go out to the big chamber to have Link and Makar fly across to the ledge straight ahead of them, watching out for the updrafts. Back in the room where we first lost Makar, a Wizzrobe will now appear to give Link trouble. Give him a nice cold refreshing Ice Arrow to get rid of him. Makar will now tell you that you can use your Hookshot on the vines, so let's do what he says and Hookshot our way toward the ledge that Makar was captured earlier, then fly Makar up there to join us. Take him through the door into another room where there are more ledges with patches of ground for Makar's seed-planting. But first off, take out the Blue Bubbles floating around where you are, then fly Makar up to some ledges to plant his vines. Be careful not to get Makar too close to a Floor Master that's on the top ledge, or he will get captured again! Link can now Hookshot his way up the ledges one vine at a time and take down the Floor Master.
Bring Makar with you through the door on your right into a caged area where there's two floor buttons to press. Have Link stand on one and Makar stand on the other. This will open up a gate ahead of you, and it will also open up a grate in the floor of the basement where the giant fan is. Now we can go further down into the basement, so get ready for the big drop!
Once you're below the big fan, go to the door that we can now unlock and pass through into the next room with Makar, where we have a combination of Stalfoses and a Wizzrobe to fight off. Pass through this room to the other door with Makar, and enter another room where we first must fight off Bokoblins and large Armos statues. Then in order to shut off the powerful air gusts, fly Makar to the other side of the gap where he can plant a vine for us to Hookshot onto. Dispose of the Floor Master in your way, then head out through the door on your right. The next room has powerful air gusts blowing at you and some blade traps moving left and right. There are also three blocks we need to push, one to get across a gap, and two to block the blade traps with. Make sure you have your Iron Boots on when you're moving the blocks. Position one of the blocks so it will trap two very-close blade traps together. With the blade traps out of your way, pick up Makar and carry him through the windy currents to the other side of the room. Through the door is another giant stone tablet that we need to have Makar play the Wind God's Aria to get rid of, revealing another door behind it. And past that is the Big Key Door, so we're already near the dungeon boss now. Blow open a teleportation pot that's near the door, and smash the pots so we can get rupees, hearts, and a fairy before we go through the door and face the dungeon boss.
Wind Temple Boss: Molgera
Makar will stay outside the chamber while Link goes inside. After he does, he sees the royal family crest disappear as sand fills the floor of the chamber. Then he sees a hideous sand serpent creature emerge from the sand and fly around flapping its mouth around before diving back into the sand. This is the dungeon boss Molgera. Its general form of attack is to emerge from a spot in the sand and snap up Link in its jaws to chew on him before spitting him out. It will also send out baby sand serpents to attack Link, and will on occasion emerge out of the sand to fly around before diving back in.
At the start of the battle, get as close as you can to Molgera's mouth without being snapped up by it and use the Hookshot to latch onto its tongue to pull it out and strike it silly with the sword. After some hits it will duck back into the sand, disappear from that spot, and emerge from another spot. When the sand around Link gets dark, quickly get out to the area that isn't dark, because that's where Molgera will emerge. When the baby sand serpents come at you, target each of them with the Hookshot to pull them out and slay them with the sword. Molgera will most likely send out the baby serpents after his tongue gets slashed and sometimes before he goes flying around in the air. Anyway, once you get the baby serpents out of the way, wait to latch onto Molgera's tongue, then pull it out and slash it again. After several successful strikes, Molgera will then fly into the air and turn into sand before exploding, turning into a Heart Container as Link dances with joy for defeating him.
After you collect the Heart Container and step into the blue light in the middle of the Triforce symbol, Makar will come into the chamber, and Link will place the Master Sword in the blue light before conducting him in playing the Wind God's Aria. The spirit of Fado will join Makar as he plays. After the song is over, Link will pick up the Master Sword, and its blade and jewel will glow and shine. The Master Sword is now fully restored. Makar says that he will stay behind in the Wind Temple to continue praying, and he wishes good fortune upon Link. He accepts as he steps into the blue light and vanishes from the temple.