Getting the Whirlwind
Step off the train and go forward. You'll find a Sound Stone. Listen to it, take out the Spirit Pipes, and play the notes. This is the Song of Healing, and it can be used once per dungeon if you need to recover all your health, but only if you are in a Temple or the Tower of Spirits. To restore its power, leave the Temple. Now you have the Song, enter the Temple.
Head north, and right past the locked door, until you come to an abyss. Pick up one of the brown bulbs. Walk over to the abyss. On the other side is a Purple Switch. You need to throw the bulb at this switch from a certain angle, at the gap in the wall, so it hits the switch. This creates a bridge that you can cross to the next area. Go south, and the door will close behind you, trapping you with some enemies, called Spinuts. Defeat all of them. A chest will appear, and two doors will open. Open the chest for 100 Rupees, then exit through the blue door.
Upstairs, go north, avoiding the purple fog. This is toxic, and hurts Link if he walks into it. Again, the door will trap you with some new enemies, known as Vengas. These are simple to defeat, but when they die, they leave behind purple toxic fog. When all are gone, a large chest will appear. Open it to find... the Whirlwind! This lets you blow a large whirlwind that can clear the purple fog and blow items across gaps. To use it, tap its icon in the top right of the screen, or hold or . Use the to aim the yellow line at your target, then blow into the mic to send a Whirlwind at it!
To the left of the chest is a fan. Stand directly in front of it and blow a Whirlwind at it. It will start spinning, and open the blue door. If any purple fog is blocking your way, blow it away. Go through the blue door. The statue here will offer to reveal the locations of hidden treasure chests for 20 Rupees. Some purple fog is blocking the door. Blow it away and go downstairs. To the right, a key sits on a pillar at the centre of an abyss. Blow it across the abyss, then run around and grab it. Go right and stand on the floor switch. The blue door will open. Go south to the locked door you saw earlier. Open it and go around to the left. Another door will trap you with two more new enemies. These are called Bubbles. You need to blow a Whirlwind at these to make them dizzy, then finish them with your sword. The doors will re-open. Go up the stairs. Head north and up more stairs. To your left is a bulb and a Purple Switch across an abyss. Blow the bulb across the abyss into the switch. It creates a chest containing a Small Key. Go back down the stairs to the second floor.
Southeast of here is a locked door. Open it, but you're immediately locked in again. This enemy, Mothula, looks hard to defeat, but not so. When it throws a skull at you, blow it back with a Whirlwind. It will get dizzy, and that's your chance to get it with your sword! Do this twice to defeat it. Go up the newly-opened stairs.
Go south from the staircase. Zelda will point out an unusual door. This is the Boss Door, and it needs the Boss Key. You can see it at the top-right of the Map, but you can't reach it just yet. Instead, continue south. To the right of this area, you can see strange blue enemies called Blastworms. When you strike it with your sword, it rolls up into a spiky explosive. Blow it into the blocks to the right to destroy them. Ahead is some purple fog. Clear it with your Whirlwind, and it reveals a path. Here, you find a floor switch, that creates a statue, a purple switch, and a chest containing a random piece of treasure. The purple switch opens a blue door. Go through it. The camera shows a purple switch blocked by some blocks, and some Blastworms. Strike the Blastworms, then blow them into the blocks, then when the switch is in the open, blow another Blastworm at it to turn it on. This opens the door to the Boss Key at the north-west of the floor. Go there.
Behind the Key is a map of the floor. Trace the path on it onto your map, since if you don't follow it, and stray into the area marked by a skull, you'll trigger several hand-like enemies known as Key Masters who will try to steal the Key. These areas are the tiles on the floor that have a spiral pattern. When you reach the Boss Door, tap it to open it. Go up the stairs. Up here are some pots containing hearts, and a sign that triggers a portal back to the entrance. It works both ways, so you can reach the Boss Room quickly. Take it if you aren't fully prepared. If you are, save your game, continue north and get ready to meet the Boss!
Boss: Stagnox, Armoured Beetle
The floor will seal the stairway once you enter. Stagnox, the Armoured Beetle, will fly down from the sky. The camera will show him from behind. This is a clue as to his weak spot. Just keep running around him until you get behind him, then blow a Whirlwind at him. This will make him dizzy, allowing you to attack the purple area with your sword. Repeat this twice. Then Stagnox will take off. He'll spit three Blastworms at you. Attack them. Wait for Stagnox to come down to attack you. Blow one of the Blastworms at him. Now you can attack him as before. Repeat the process until Stagnox is defeated.
The Symbol of the Forest Land will appear on the ground, and a pedestal will rise from it. The green Forest Source will rest on it, and blue light will travel from the Temple to the Tower of Spirits. Some of the energy has returned to the Tower, and one its sections has been restored. A large chest and a blue portal will appear. Open the chest for a Heart Container. Now step into the light, board the train, and set a route to return to the Tower of Spirits.