Return To The Tower
A cutscene will show energy coursing along the Spirit Tracks from the Fire Temple to the Tower of Spirits, and then the topmost section will now be joined together, fully restoring the tower to its original appearance. This will also give us more floors to explore in the tower.
Now that we're back on the train, a new track has appeared that will help us get back to the Tower of Spirits faster. Plot a course using the new track and get the train rolling back to the tower.
Tower of Spirits
Once you return to the ground floor room of the Tower of Spirits, go back up to the winding staircase, and then travel up the staircase to the new door that's opened up and you'll start your next search on Floor 18.
The first Tear is in a Safe Zone in the southeast section behind a bunch of blocks you need to bomb. You need to have already gotten Bombs in order to bomb the blocks; otherwise, leave the Tower of Spirits and go find Beedle to get a Bomb Bag. While watching both the Phantom that goes around in a circle as well as the one that goes north and south along the east passageway, bomb the blocks to get to that corner so you can grab the first Tear.
There's a locked door at the north end of this floor; however, getting the key requires getting to the floor button at the north end from the west passageway to make a treasure chest appear, then going over to the east passageway and whip-swinging across one post to get to the chest. This will mean more block-bombing and a lot of patience and watching the Phantoms moving around the floors. Once you get the key, open the locked door and head up the staircase to Floor 19.
The next Tear is located at the south end of this floor behind some blocks to bomb. The problem is that there's a gap that we need to cross in order to get there. The solution: go over to the northeast corner and grab the arrow redirect, then head to the west end of the floor past the Miniblin riding an Armos statue and place it on the Force Gem statue tile near the door on your left, striking it so that it's aiming to the left. Then go over to the floor button north of the tile and stand on it, causing the door to stay open (if you get off the button, it will close back up). Beyond the door is another arrow redirect we need to hit with the Boomerang so that it's now aiming north to a red eye switch. Then, while still standing on the floor button, aim for the arrow redirect on the east side of the door, which will cause the arrow to fire into the other redirect and then be fired into the eye switch. A bridge will now appear on the east side of the floor crossing the gap to the south end.
Now go over to the east side, moving past more Miniblins riding Armos statues, and cross the bridge to the south end so you can head left toward the Tear of Light. Once you do, however, a new kind of Phantom called a Wrecker Phantom will appear to the right of you. When it sees you, it will turn itself into a ball and plow its way through blocks and anything it is able to destroy, and if it hits you, you lose a heart and must start over at the entrance of this floor.
To get the Tear, place a Bomb near a block where you can get it very quickly once it's blown away. Then bomb the blocks between you and the Safe Zone in the southwest corner of the floor and enter the staircase there to Floor 20.
The last Tear is behind a closed door on this floor that we need to open by hitting a red eye switch behind another closed door that opens and closes with the press of a nearby floor button. So we need to use some arrow redirects to get the arrow where it needs to go. Not making this any easier is that there are two stacks of blocks in the area we're dealing with: one that has an arrow redirect on top we need to place somewhere and another which will block the traveling of the arrow. And if that's not enough, there's also a Wrecker Phantom patrolling the center of the room.
First of all, let's deal with the blocks. There's two ways we can go about destroying them. The first way is that we can use Bombs to blow them up, which can be time-consuming as well as bomb-consuming. The other way, which is risky, is letting the Wrecker Phantom see you so you can make it plow through the blocks to destroy them. Whichever way works for you, first move the moveable block so that it's between two platforms in the upper right corner of the room you're in. Then grab the arrow direct and leap across the block to the platform with the Force Gem statue tile on it and place the arrow redirect there, making sure that it's aiming to the south. Then go over to the platform on the west side of the room and use the Boomerang to redirect an arrow redirect southeast of his location so that it's aiming to the north. Then go over to the platform where the floor button is and, while standing on it to keep the door open, fire an arrow at the arrow redirect that's now to your left. If set up right, the arrow will go through all three redirects and into the eye switch behind the door, opening the other closed door where the Tear of Light is behind.
Now grab the Tear of Light to power up Link's sword, then sneak behind the Phantom to strike it from behind and have Zelda possess its armor. She can now use that form to turn herself into New Hyrule's answer to Samus Aran and plow through anything she can destroy. Take her with you back to Floor 19 the same way you came.
Have Zelda go ahead first into the east side of this floor to take out the Miniblins riding the Armos statues. Then follow as Link, watching for the Wrecker Phantom moving around the southeast corner, until you reach a door to your left that's blocked by inactive Armos statues. Plow through all of them as Zelda so that Link can enter the room with her. Have Link stand on top of the stairs where a floor button is and redirect the arrow redirect that's northeast of his location with the Boomerang so that it's aiming north. Then fire an arrow at the redirect so that it's aimed at the eye switch. This will cause a treasure chest to appear which contains a random treasure. There's a locked door in this room to your right that we can't open just yet. Instead, take Link and Zelda back down to Floor 18 through the stairs to your left.
Now we're in the center part of this floor where, for the most part, we need to push blocks onto some floor buttons in the four corners to keep them pressed down. While Link can move the smaller blocks, Zelda can move the bigger ones, and you're going to need her to move the bigger ones in order for Link to move the smaller ones at certain points. Basically, we need to have a big block pushed on top of two floor buttons in the upper left corner, a small block in the lower left corner, a small block on one of the two buttons in the upper right corner, and a small block in the lower right corner. Lastly, have Zelda stand on the other floor button in the upper right corner. This will disable some spikes barring your way to a chest near the south end of this room where you can find the small key. Take it and Zelda with you back to floor 19 to unlock the door and go up the staircase back to Floor 20.
Now we're on the east end of this floor. Go south and you'll come across a hallway full of rolling boulders. Have Zelda go before Link to roll through the boulders to give him a clear path to the door at the left near the north end. Go to the left and strike the nearby switch orb. Zelda will notice that there's a lake of lava that she isn't able to carry you through in the Wrecker Phantom form. Instead, direct Zelda to go south down a hallway full of destructible blocks until you reach a staircase that takes you to Floor 21.
In the room that you enter on this floor, have Zelda stand on one floor button and Link on the other. The door into the room will now close, and you will now have four Stalfoses in there to defeat by using the Whip. These will be followed by three Zora Warriors, which Link can handle by using the Whip to remove their shields before taking them head-on. During this part of the fight, a rat will run around Zelda, causing her to cringe. Don't worry about it until you're done with the Zora Warriors, then slay it with the sword. The closed door will now reopen, so you can head back into the Safe Zone near the staircase. However, the room will now have four Phantoms moving around in a clockwise circle near the outer walls. Carefully sneak behind one and strike it in the back. Zelda will now jump into that Phantom form so you can now take her back to Floor 20 to cross the lake of lava.
At the lake of lava, we need to arrange two arrow redirects in two strategic places: one so that it's aimed toward a eye switch located on an east wall, and one that's aimed toward an arrow redirect behind a closed door that will redirect the arrow toward another eye switch to open up the door where the other staircase to Floor 21 is. Work with Zelda so that you can get the two arrow redirects where you want them, having Zelda holding the one aimed toward the door. Then from a strategic spot fire an arrow into the redirect aimed at the east wall eye switch first so you can open the door and quickly fire an arrow into the redirect that Zelda is holding. When you're done, have Zelda join you east of the lake of lava so you can have her drop the arrow redirect by whipping her, then let her carry you across the lake to the now-opened door to the staircase.
There's nothing in the room that you've reentered this floor on that you need to worry about or get, just some pots and nuts to break for restoring hearts and weapons. Head east and then south to the staircase going up to Floor 22.
There's an electrified Big Key you need to have Zelda carry over to the Big Key Door in the southeast corner of this floor, so direct her to avoid the sand patches and to go through the walls of fire so she can reach the key. Join her when she does get the key, because Key Masters will start to pop up. Go before Zelda part of the way to fend off some Key Masters with your arrows, then direct Zelda to go along a passageway on the north end of the floor to a metal platform with a circle on it. While she heads there, use arrows to take out the Key Masters in her path. Then have Link stand on another metal platform with a circle on it so he and Zelda can swap places, then direct Zelda over to the Big Key Door to throw the key into the lock. When that happens, the Key Masters will go away, and so will the walls of fire, giving Link a clear path to rejoin Zelda at the door to the staircase to Floor 23.
Up ahead are some big doors that will require Link and Zelda to push open together. Once you do open the doors, a blue portal will appear to the right that will take Link and Zelda back out to the main staircase. Use it to save your progress before you head up the stairs beyond the doors to face the Tower Boss.
Tower of Spirits Boss: Byrne
As Link and Zelda enter the room, Byrne greets them by congratulating them on restoring the Spirit Tracks, but he tells them Malladus' resurrection is near, and he will do everything in his power to keep the two heroes from stopping it. He raises up his gauntlet, preparing himself for a fight.
At the beginning of your battle with Byrne, he will jump from pillar to pillar and stop to fire bolts at you. Dodge these and wait for him to fire his gauntlet toward the ground. Dodge that and have Zelda grab the gauntlet to pull Byrne down from the pillar so you can give him some good strikes with your sword. If Byrne grabs Link or Zelda with the gauntlet, have the other come over to free the captured partner. After the second time of doing this, Byrne will now stay on the ground and block all your sword attacks but the third one, after which he will charge up an attack towards Link. While he's charging up, quickly get Link out of the way and direct Zelda toward Byrne so she can hold him off while Link strikes at him from behind. Repeat this tactic until Byrne is defeated.
After Byrne is defeated, he fumes at the thought of being beaten by two human children. Zelda responds that though she and Link may be human, they were able to accomplish together the impossible. The two heroes share a happy moment of triumph together that quickly sours as Byrne makes a run for it to the top of the tower. Zelda and Link snap out of it and chase after him.
Take Link up the winding staircase to the top of the tower. There Link and Zelda will see that Chancellor Cole has completed the resurrection of Malladus in Zelda's body. Byrne now asks for Malladus to give him the power he desired. Instead, Malladus blasts Byrne into unconsciousness. Cole sneers at Byrne's foolishness and leaves him with Link and Zelda while he takes off with the resurrected Malladus, who has yet to have full control of Zelda's body, on board the Demon Train, much to the frustration of Zelda.