In your first visit to the Tower of Spirits, you meet Anjean. When the automatic scenes are over, go up the stairs in the north part of the room. Then head up the curved staircase and go through the door.
After you make your way in, a giant monster in a suit of armor appears. Do as Zelda says and run back the way that you came. You'll automatically go down to where Anjean is. She will tell you how to defeat the Phantoms. Collect the three Tears of Light, then hit the Phantom in the back.
Go back up to where you encountered the Phantom. When you get to where the path splits, go left and step on the shining part of the floor to the left. This is a safe zone, where the Phantoms can't see you or hurt you.
Go left from the safe zone to find the first Tear of Light. Then head back to the central area and go up, then up through the safe zone and up to the safe zone at the top of the room to get the second Tear of Light.
Next, go down from the safe zone but immediately go to the right, and keep going until you reach a switch. A bridge to the third tear of light appears, but it is only temporary. Run to the left, then down, then to the right, and go across the bridge to get the third Tear of Light.
Once you have all three, secretly run up behind the Phantom and hit it in the back.
An automatic scene will take place. Now that Zelda is possessing the Phantom, you can use her to help you solve the puzzles in this place. You can control her just like you did in the castle when you were trying to sneak around the guards.
Draw a path from Zelda into the door and an X mark will appear over it. Then when Zelda is pushing the door, tap on the other door so that Link pushes it on his side. Together you will push open the door. Go up the stairs.
With that armor, Zelda can walk across spikes. Draw a path from Zelda across the spikes and over to the switch to the right such that there is an X over the switch. Zelda will walk over and hit the switch, lowering the spikes.
In the next area, there is a door near the bottom of the area that will only open if both switches are down, so draw a path from Zelda to the other switch and the door will open. Have Link go through the door and push the block in front of the rat hole. Be sure to kill any rats that get in the way or are hanging around after you push the block.
There are spikes blocking the path. As Zelda approaches them, she realizes that the enemy Phantom might not attack her because it might think that she's on its side. Have Zelda walk across the spikes and then hit the switch behind the Phantom, then have Link walk across where the spikes were.
Now have Zelda talk to the Phantom to distract it, and then have Link run up and hit it in the back. Then tap on it, and Zelda will switch Phantoms. The old one will disappear.
Now the two of you can go upstairs. Head up to the platform and tap on the thing that is floating there: the Forest Rail Map. Step into the blue portal that appears, and then talk to Anjean. She will say that you need to find Gage at the Forest Sanctuary before you can reach the Forest Temple.