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Return To The Tower
A cutscene will show energy coursing along the Spirit Tracks from the Forest Temple to the Tower of Spirits, and then the lowest floating section of the tower will now be joined to its base. This will give us more floors to explore in the tower.
Now that we're back on the train, some new tracks have also appeared, some of which will help us get back to the Tower of Spirits faster and avoid the Lost Woods altogether. Plot a course using the new tracks and get the train rolling back to the tower.
As we head back to the main three loops, however, we'll see that some of the trains have been turned into Dark Trains, powered by evil spirits. We'll need to avoid running into those by watching their movements on the tracks, replotting our course when necessary.
Another thing that we'll see appear on the main loops is an archway. We'll find out exactly what these archways are as we progress into the game.
Tower of Spirits
Once you return to the ground floor room of the Tower of Spirits, go back up to the winding staircase, where Zelda notices that they ascend higher to another door. Travel up the staircase to that door and you'll start your next search on Floor 4.
Again we need to get the three Tears of Light and then have Zelda possess one of the two Phantoms on this floor. One of the Tears is on a platform in the middle of a pool of lava which one of the Phantoms travels through. Wait for the Phantom to start crossing through the pool, then stand south of the pool and use the Whirlwind to blow the Tear over to the other side of the pool. Watch out for the statue faces that spew flames and wait for it to cease before passing as you head over to the other side to get that Tear.
Another Tear is located in a Safe Zone in the upper right corner of the room. You can easily grab it after getting the Tear that you've gotten from the lava pool.
The third Tear is located in a Safe Zone in a lower left corner just west of the lava pool. Here, though, you'll have to watch out for a statue head that constantly spews flame. Your only chance of getting past that is to wait for the Phantom patrolling the hallway to walk in front of the statue head, blocking its flame for a while, then rush into the Safe Zone and grab the Tear.
Now we can stun a Phantom and commandeer its armor for Zelda to use. Your best bet is to go after the Phantom patrolling around the lava pool, making sure you can get safely behind it to strike. You can use the Safe Zone to the lower left of the pool to wait for the Phantom to get close before striking.
Now with Zelda as the Phantom again, bring her over to the lava pool in the middle south of the floor and direct her to go into the pool first. Then get Link to jump onto her shield and direct her to carry you to the other side where you can get off. Now summon her to go through the door and up the stairs to the next floor.
Lead Zelda to the lava pool in the south middle of that floor and have her carry you over it again. This time we'll need to direct Zelda to two propeller pillars that are in the lava pool: one on the left side near the middle and one at the top part. This will get a door to open that leads to a hallway on the west side of the floor. While riding on Zelda's shield, slay the Keese that are flying around. You can direct Zelda toward a treasure chest located on the left side of the pool that will give you 100 rupees as a reward.
Now get Link and Zelda toward the door and lead her to a cross-square room in the lower left portion of this floor where a Spinut runs around with a small key. Link won't be able to slay it by himself because it will run off faster than he can hope to catch up to it. So the object is to get Zelda placed where both she and Link and cut off its escape and then slay it. This will give us the small key that we need to open a door to a small lava pool that we must get across to reach the door to the staircase leading to the next floor.
As soon as Link and Zelda enter the first room on this floor, the door closes up behind them. A Zora Warrior will suddenly appear. This enemy will require you to direct Zelda to attack it head-on while Link goes to strike it from behind. Succesfully defeating it together will cause the door to reopen and another door on the right to open. Go through that door and lead Zelda down to the room on the lower left of this room, where you'll see a Miniblin riding on top of an Armos. We cannot defeat it yet, so have Zelda block the flame of a statue head as Link goes into the room on the right where he can go onto a platform and direct Zelda to stand next to the platform so he can jump onto the shield and she carries him. Then head back into the room in the lower left directing Zelda to get close to the Armos so Link can blow the Miniblin off it with the Whirlwind, and then jump down and slay the Miniblin, also causing the Armos to blow up. Get Zelda to give Link a ride again, and then direct her to travel along a passageway near the lower right section of the floor to get past flame-spewing statue heads and also to get high enough so Link can use the Whirlwind to blow a small key down for him to grab. Jump down, get the small key, and then direct Zelda to block the flame spews as you head back the same way you came. Then go into the room in the middle of the floor and avoid the Miniblins on Armoses to open up the locked door with the key, leading Zelda up the staircase to the next floor.
Link's sword loses its glow again and Zelda is again free of the Phantom armor as they enter this floor. Here we can get the Snow Rail Map, which unlocks some Spirit Tracks leading to the Snow Realm, the next area we need to travel to. Step into the blue portal after getting the Rail Map to return to the ground floor.