Before returning to the Tower of Spirits, go back to the Forest Sanctuary. Once you are there, go to the left from the train platform to find a small raised area with a chicken and a treasure chest on it. Go up the steps to the left and use the Whirlwind to blow the chicken off of the platform. Run over to the chicken and pick it up, then go back up the same stairs and jump off of the ledge toward the treasure chest. With the chicken, you will be able to jump across and reach the chest. It contains a big red rupee, worth 200 rupees.
Now leave the Forest Sanctuary and set your course for the Tower of Spirits. There are some evil trains on the tracks now, so be sure to avoid them. They can change direction to try to run into you, so watch their direction arrows to see which way they are going. You might have to update your route several times to keep away from them.
Tower of Spirits
Once you reach the Tower of Spirits, go up the spiral staircase. It has become longer since you defeated Stagnox. The stairs will take you to an area that you couldn't reach before.
In the new area, two Phantoms will appear. First, go to the right, but be careful to wait for the statue to stop spitting fire. After you pass the statue, go north. You can hide out in the safe area to the left if necessary. Otherwise, continue north until you see lava and a Tear of Light to the right. Use the Whirlwind to blow the Tear of Light away from the lava. You can also stand to the south of the Tear of Light and blow it to the top area instead.
Avoid letting the Phantom see you, and run over to the three Tears of Light. When you run up to the right of the lava, be sure to get the treasure chest to the right. It contains a treasure trading item.
Go around and collect the Tears of Light, being careful to avoid the other Phantom and the fire-breathing statues. There is a statue on the far left that constantly breathes fire, so you will have to wait for the uppermost Phantom to walk in front of it before you can safely pass by. Once you have all three Tears, run up behind a Phantom and hit it with your sword. It is probably going to be easier to run up behind the lower Phantom because of the statue on the left that constantly breathes fire.
With Zelda as a Phantom, go to the bottom-middle area of this floor. There is a big lava zone here that you can't pass. However, Zelda can go into the lava safely as a Phantom. Have her walk into the lava, then have Link jump onto the Phantom. Zelda will raise the shield for you to jump onto. Now have Zelda walk to the right and onto the safe floor, where you can double-tap to make Link hop off.
After you're both on the other side, call Zelda over and go together up the stairs.
Up here on the fifth floor, there is a huge lava area in the middle of the room. Link will need to hop onto Zelda's shield to get across, but first, have Zelda go around and kill the Keese that are flying around. Just draw her path onto the Keese and she will use the sword to kill them.
Once the Keese are dead, have Link hop onto the shield. First, go to the bottom left of the room where Link can open the treasure chest to get a big green rupee, worth 100 rupees.
Next, there are two propeller switches, one on the left side of the room and one in a hallway at the top. Have Zelda go over to each one and have Link use the Whirlwind to activate each switch. Once you do, the door will open. Go through with Zelda.
There is an area in the north part of the room with some lava and a tall ledge that looks like you could hop onto it from Zelda's shield, but it's too high, so don't worry about this area for now.
Next, there is a monster in the bottom-left part of this floor that is marked with a skull on the map. You have to kill it, but it runs away when it sees you. You will have to put Zelda somewhere in the maze where the monster will run away from her, then have Link run to where it is going. Eventually the two of you can trap the monster and you can kill it to get a small key.
Call Zelda over and go up and unlock the door. Then have Zelda walk into the lava, and have Link jump onto the shield. Get Zelda to the top of the room and have Link hop off, then call Zelda and go up the stairs.
As soon as you get upstairs, the door will lock behind you and a Geozard will drop from the ceiling. To defeat it, draw a path from Zelda to the Geozard. When she hits it, have Link hit the Geozard from behind. Repeat this until the Geozard dies.
With Zelda, go through the door that unlocked. There is a Miniblin ahead, but it is on top of an Armos Statue and Zelda can't reach it with her sword. You and Zelda will have to go to the right side of the room where there is a ledge. However, there is a fire-breathing statue in the way, so have Zelda stand there while Link runs past. Once you get past, have Link go onto the ledge and jump onto Zelda's shield from there. Then have Zelda walk back over to the Miniblin, and tap it when you're close by so that Link hits it with his sword. Be sure to run away from the Armos Statue after you defeat the Miniblin, because the statue will explode.
Next, go all the way to the bottom right corner of the room. Link needs to stay on top of the shield, but be careful, because one of the fire-breathing statues is tall enough that it will hit Link. Wait for that tall statue to stop breathing fire, then have Zelda go past. Finally, you will get to the right side of the room where Link can use the Whirlwind to blow the key off of the platform.
With the key, return to the middle of the room using Zelda to protect Link from the fire-breathing statues. Go up to the door in the middle area and unlock it. There are Miniblins on statues here, but you can just run past them and ignore them.
On the seventh floor, Zelda will exit from the Phantom and it will disappear. You can go up and get the Snow Rail Map. Use the blue light to get back to Anjean. Talk to her and she will tell you to visit Steem in the Snow Sanctuary. The train will go outside.