Kakariko Village in trouble:

After the short story sequence look around on the island you are standing on and find a plaque that talks about shooting into the morning sun.  Use the Song of the Sun to make it night, then wait until dawn and shoot an arrow into the rising sun.  A fire arrow will drop down onto the island across the water from you.  Go get it.  Now go to Kakariko Village using whatever method you like and as you walk in, you'll see...we'll I'll let you see for yourself.  Sheik will teach you the Nocturne of Shadow here.  Use it to warp to the entrance of the Shadow Temple.  Go in the cave behind you and you'll see a ton of unlit torches.  Stand on the platform in the middle and use Din's Fire to light all the torches simultaneously and open the gate to the Shadow Temple.

Shadow Temple:

If you haven't already gotten it, go back to the Quest for Truth section and get the Lens of Truth.  You need it for this level.  Go down the hall and turn the corner, use the hookshot to get across the pit, and you'll see a wall in front of you.  Walk through it.  Immediately turn left and follow the wall two face tiles down and walk through the wall again (use the Lens in any area to see where the walls can be walked through).  Now go through the hall and door and go through another wall to come to a room that seems to have no exit (but we know better right?)  As soon as you enter head right and follow the wall until you find an opening (use lens if you want).  Go through the door behind it and then play the Song of the Sun to stun the zombie and kill it, then hunt down and kill the two bats.  Get the chest that appears for the Dungeon Map.

Now go back out and head right following the wall to an opening behind a walk-through wall with a pot on either side of it.  Keep going down this tunnel and you'll end up in a room that looks the same as the last one.  The opening to go through next is in the corner on the right with a pot beside it.  Go through the door there and you'll face Dead Hand, which is the same guy that you killed to get the Lens of Truth in the bottom of the well.  After this easy kill, a chest with the Hover Boots will appear.  Snatch your prize then go all the way back through to the first big room that had the statue in the middle of it.

Use your Lens and look at the skulls on the pillars around the circle, and see which one does NOT disappear with the lens.  Now walk up to the tab sticking out of the side of the base of the statue and push the statue until the tab you are pushing is pointing toward the skull that didn't disappear. Don't stop pushing until it gets there or you'll fall in a pit.  Now put on your hover boots and walk across the pit to the tongue-looking platform and go in the door and down the ramp.  Kill the laser eye in the middle of the next room by throwing two bombs at it, then stand in the middle of the round platform it was on and play the Song of Storms for a Big Fairy (Big Faeries heal both life and magic but can NOT be captured into a bottle.