In the Tower, you meet Anjean, who says that Malladus intends to possess Zelda's body. Zelda is furious, and determined to stop this. Anjean tells you that you need to make the Spirit Tracks reappear in order to get what you need to defeat Malladus.
The Tower of Spirits holds Rail Maps that will help restore the tracks, but to get those maps, you need to fix the broken tower. And to do that, you need to go to the four temples around the world. Your objective now is to get the first rail map, the Forest Rail Map, which is accessible in the part of the Tower that is still on the ground. This will give access to the Forest Temple. Anjean tells Zelda to go along with you to help in your quest.
Go up the stairs at the top of the screen to find yourself on the winding staircase that goes up the Tower of Spirits. Climb that staircase to get to a door. Go through that. Go in a little way and a Phantom will appear. Follow Zelda's advice and go back out the way that you came. Talk to Anjean again.
Anjean tells you that in order to bypass the danger from the Phantoms, you will have to collect three Tears of Light, which are in different places around that room that you just escaped from. Once you gather all three, your sword will have the power to stun a Phantom if you hit its back with your sword.
Go back up to that room in the Tower. Go toward the left and you'll find a Tear of Light that is pretty easy to grab. Zelda and Anjean will let you know that the shiny purple floor zones are areas where Phantoms can't detect your presence. Standing on one of those regions will keep you safe from the Phantoms.
Now continue to the top area, and there is another Tear of Light there. Continue on to the right and hit the switch here, then quickly run around through the middle area of the room, avoiding the Phantom, to run across the bridge before it goes away. Now you have the third Tear of Light. Your sword is powered up, so go over to the Phantom, being careful not to make a sound or let it see you, and hit its back with your sword.
It looks like you're in danger, but Zelda flies into the Phantom and possesses it with her spirit. Amazingly, Zelda can walk around and control the Phantom. You can control her just as you did earlier in the castle when you were helping her sneak out.
Now that Zelda is controlling a Phantom, go to the large double door in the center of the room and have her push on one side of the door. Then you need to push the other side of the door at the same time. This will open the door.
On the next floor, you'll discover that your path is blocked by spikes. But as a Phantom, Zelda can walk right over those spikes and not get hurt. So have her walk over those spikes to the switch, which she can hit with her sword to lower the spikes.
Next, head south with Zelda, and have her stand on one of the switches by the door while you stand on the other. The door will stay open. As you continue on, rats will surround Zelda, who is too scared to go any farther. Kill the rats and Zelda will be able to continue. And then push a block in front of the rat hole to stop the rats from coming out and impeding your progress (you can't leave the room without Zelda, so don't even think about leaving her there).
Now, have Zelda walk over more spikes to reach a switch that will lower the spikes for you. Have Zelda talk to the Phantom in this area so that it won't see Link. Then have Link hit the back of this Phantom, and tap on it. Zelda will depart from her current Phantom and inhabit the Phantom that you just stunned. The previous Phantom body will become lifeless, collapsing to the floor and then disappearing.
Now you can go upstairs. Once you do, Zelda's Phantom body will deactivate and disappear, and Zelda's spirit will be floating around once again. You are in a safe room where the Forest Rail Map is waiting. Go get it, and you'll see some Spirit Tracks reappearing on the map. Step into the shining blue light and you'll go back to where Anjean is.
Anjean tells you that although you restored some Spirit Tracks, you will have to restore even more to be able to reach the Forest Temple. There is a Forest Sanctuary in this realm where another Lokomo lives, and the all of the members of the Lokomo tribe can help restore the tracks, along with the power of Zelda's Spirit Flute. So your objective now is to go to the Forest Sanctuary. Since you don't have a train, Anjean lets you use the Spirit Train.