Out here, you will encounter Spinuts. These enemies are easy to defeat. They charge at you when they see you, but not that quickly.
Kill the Spinuts that have surrounded the soldier, then talk to him. He'll tell you to examine the wall, so head north.
You'll pass by a bomb flower, and if you keep going right, you'll encounter another bomb flower. There is a hidden tunnel that you can reveal if you place a bomb against the flat wall that is sort of half way between the two bomb flowers.
In the first room inside, there is a puzzle. Go to the right side of the room and pull or push the block onto the brown switch on the top-right side of the room. This will open the blue gate at the top-right, which has a key behind it. Take the key over to the locked door in the middle of the back wall and go upstairs.
On the next floor, there are some water areas that you need to jump over. To get over the water, just put the stylus on the other side, and Link will automatically jump across.
Up ahead, you need to activate the switches in a particular order. You should use the map feature to make note of the clues in this room.
Get the 20 rupees from the chest, then use the bomb flowers to get rid of the barrier in the path.
The correct order to hit the switches is:
2 4 1 3
When you hit them in that order, the door will open and you can go up to the next floor.
On the next floor you find out that Zelda is afraid of rats. Kill the rats or you won't be able to go farther!
Soon you will reach the stairs, and some automatic scenes will take place before you end up in the Tower of Spirits.