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Path To The Tower
Now that you're outside the back exit of the castle, you'll encounter some Yellow Spinuts that you can easily slay with the sword. You'll also see a guard you can talk to who'll tell you there's a tunnel hidden behind the north wall that will lead you to the Tower of Spirits. Pick up a Bomb Flower and place it near the wall where you think the tunnel entrance is. If done right, you'll blow a hole in the wall into which you can enter.
On the first floor of the tunnel there's Keese and Red Chuchus that you can easily slay. There's also a floor button on the right side of this floor that will open a door, but you'll need to push a block on top of it to keep it open. Fortunately there's a block nearby; use Link to push the block onto the button to keep the door open. Behind the door is a chest that contains a small key. Use the small key to open the other door. Now you can proceed to the...
There's a series of stone tablets you can read that will give you a clue to the next puzzle you'll need to solve. Proceed all the way to the right and use the Bomb Flowers to blow up blocks that are between you and the next room, where you see four switch orbs which are part of that puzzle. Slay the Spinuts first, then hit the switches in this order: east, north, south, west. (This is a timed puzzle, so hit the switches before time runs out.) This will open up a door that will lead you to the...
Slay the Keese and go north. Soon Zelda will pop up in the open and then two rats will run around her, scaring her. Just quickly slay them and head to the exit to the north.
Tower of Spirits
As Link and Zelda approach the Tower of Spirits, they can see parts of the tower still floating in the air. After they enter, they will see the statue of a train which an old lady named Anjean says is the Spirit Train. Here we enter a cutscene where Anjean tells Link and Zelda what the Spirit Tracks do, and that Malladus, the evil spirit held imprisoned by the Spirit Tracks, needs the body of Zelda to be resurrected in. Zelda is enraged by this news and demands to know how to stop this. Anjean tells her that the only way to stop Malladus is to restore the Spirit Tracks that lead to the four temples in New Hyrule, and to restore them they must find the rail maps that are in the Tower of Spirits. Unfortunately, Link cannot enter the Tower of Spirits alone, and as Anjean is too busy with trying to keep the tower together to accompany Link, she suggests that Zelda should go with him into the tower to find the rail maps.
Leave the room by taking the stairs to the north, then go up the winding staircase to the first door. You'll now be on the first floor of the tower. Zelda will comment on the big doors that they see, but immediately appearing in front of them is a Phantom who will come in after Link. Quickly leave, and you'll enter a cutscene where Anjean will tell Link and Zelda that he needs to collect the Tears of Light and then hit the Phantom in the back to stun it for a while. The Tears of Light will be located on the first floor, so finding them won't be hard; it's getting them that will be the trick.
The Phantom we've seen earlier will move in a clockwise pattern around the center of the room. Stay out of its sight as you move clockwise around this floor to collect the Tears of Light, using the special-tiled floors called Safe Zones to keep yourself invisible and untouchable by the Phantoms, who will take one heart away from your life meter and cause you to start over from where you entered the floor if they touch you. Start with the Tear of Light in the west room and then move to the one in the north room. In the north room, there's a switch orb you must hit to activate a bridge across a gap in the east room for the third Tear. Quickly move into that room and across the bridge to gather the last Tear. This will cause Link's sword to glow. Now get behind the Phantom and strike him with the sword. You'll enter a cutscene where the Phantom turns around and gets ready to slay Link, but Zelda enters into the Phantom and possesses its armor, frightened at first but then realizing the potential she has in this form.
Now with the both of them appearing before the big doors, direct Zelda as the Phantom to stand at the right door while Link stands at the left door, then direct Zelda to push the door forward. You'll also have to have Link push his door forward at the same time. Both doors will open and the two of them can now go to the next floor.
Proceed to the right, and up ahead you'll see spikes that Link cannot walk across -- but Zelda as the Phantom can. Direct her to walk past the spikes toward a switch orb she can hit with her Phantom sword so Link can walk safely through and summon her to follow him. Now head south and slay the Spinuts, then get Link to stand on one floor button and Zelda to stand on the other. The door right next to them will open, and they can walk now to the left where Zelda cringes in fear as rats emerge from a hole. Quickly slay the rats and push the block to cover up the hole, then head to where there's another set of spikes that Zelda needs to walk past to deactivate with a switch. Blocking that switch, however, is a Phantom. Direct Zelda to walk past the spikes, deactivate the switch, and distract the Phantom's attention so Link can rush safely past them, hitting the Phantom in the back to stun it. Then summon Zelda to follow you through the door to the next floor.
Here Link's sword loses its glow and Zelda is now free of the Phantom armor as it vanishes. This floor contains the Forest Rail Map that brings back not only the tracks that were first lost in this region, but also brings forth new tracks leading to other places which we'll need to go to. A blue portal will appear that will take you back to the ground floor, where Anjean causes the Spirit Train to transform from a statue into a functioning vehicle for Link to use.