Go up the stairs and turn right to see a giant block that you could not push previously. You can push it now that you have the Silver Gauntlets, so push it straight ahead until it falls into a gap ahead.
Enter the Temple
Up ahead you find a Razor Trap and Beamos. Bomb the Beamos, then look at the ceiling; there's a crystal switch hanging down. Use the longshot to activate it, then go through the left door.
Kill the Wolfos in here. Stand on the Triforce symbol and play Zelda's Lullaby as usual to make a big chest appear. Longshot to it to get the compass. To get back across to the entrance, you can longshot the brick climbing wall. Exit.
Now go through the open door on the right. Inside are some rolling boulders and five silver rupees hidden around. Get the first one with the Hover Boots (or jump off the ledge and do a jump attack at it). The others are hidden in niches in the wall. Avoid the rolling boulders to get them, and play the Song of Time to remove the blue block, killing the gold skulltula in this niche. Play the Song of Time to move the block again, getting the last silver rupee. Go through the door that opens.
BE CAREFUL! A Like Like will drop from the ceiling in this room. Kill it, then grab the small key from the chest and go back to the room with the razor trap and beamos. Go through the locked door.
The pots in this room will fly at you. ANOTHER Like Like drops in, so kill this one, too. Then go to the end of the hallway and climb up the brick wall to the next room.
CAREFUL again! Use the Lens of Truth right away to see the Wallmaster here. Kill it (remember that Din's Fire is effective). Grab hold of the left-hand handle of the mirror to push it toward the sun switches. There are four: the first makes a chest fall containing a recovery heart, the next makes a trap chest fall that freezes you if you open it, the next opens the door, and the third releases a nasty wallmaster! So push the mirror to shine at the first two suns, ignoring the chests, and shine on the third sun to open the door. Don't go any further or you'll release that wallmaster. Exit.
Now you're in the big room with the statue where you got the map so long ago. Don't touch the Armos! It's real! Go up the stairs and use the Hover Boots from up here to reach the statue's hand. (If you fall below, longshot the target above the real Armos). Once on the hand, play Zelda's Lullaby to make a chest appear in the other hand. Longshot it for a small key. Then longshot the torch on the ledge near this hand, turn around, and play Scarecrow's Song to make Pierre appear. Longshot him so you can get the gold skulltula on the far wall. (A pot might float way way up to where you are and try to hit you, so be careful.) That's the last gold skulltula in this dungeon! You should be close to 100 now.
Fall below and use the longshot target above the real Armos, and climb up above. Use the longshot on a small chest on the far ledge across the way (it just contains five rupees), then hammer the rusted switch behind it to open the central bars below. Fall below and go through that central door.
Push the giant block forward until it falls, push the next block, then hammer the rusted switch here to create an elevator. This will go down to the room where you can exit the temple, giving easy access to the heart of the dungeon if you want to leave for a while to replenish things and such. Return to the big room with the big statue.
Use the longshot target above the real Armos again, and go up and unlock the door above.
Go through the corridor, killing the Beamos with a bomb to get past safely.
In the next room there are many holes. There is a Beamos here, as well as three Anubis. If you have neither Fire Arrows nor Din's Fire, you will have to use the Song of Time in one of the larger holes to reveal blue blocks, step on the switch, and lure the Anubis into the fire. Otherwise, just kill them with Fire Arrows to wipe them out easily. Kill the Beamos and go through the door that opens (near the floor switch).
This room can be tricky; there is a switch here that won't stay down. You have to awaken an Armos and make it walk onto the switch, then QUICKLY go through the newly-unbarred door. The door you want is NOT the one near the sun switch. Get near the other door, and awaken the top-right Armos (from this perspective), and it should jump on the switch. Quickly go through the door.
In this seemingly empty corridor are two hidden chests that will be revealed by the Lens of Truth (you can guess their locations from the map if you have the compass). Both just contain a recovery heart, which you will need, because in the next room is another...
Iron Knuckle (II)
Shoot an arrow at the Iron Knuckle to awaken it from afar. Just beat it like you did before. With the Master Sword, it will take far fewer hits before it dies. With Biggoron's Sword, the battle is a piece of cake!
Once it is gone, go through the unbarred door behind the throne and go outside to find another big chest. This one contains the Mirror Shield! It reflects light and can deflect beamos beams!
Go back to the room with the four Armos and go past the razor trap. Stand in the light and press R to raise your shield, using the control stick to shine it on the sun switch. Go through the door that opens to get a small key.
Go back to the Anubis room and unlock the door across the way. Kill the two beamos, then longshot the skulltula on the moving climbing wall. You don't have to bother trying to climb up the wall; just use the longshot on the top piece to get above the moving portions. Kill the two beamos up above, then go around the side and through the door.
Play Zelda's Lullaby to open the barred door, and go through. Kill the torch slugs, then use the hammer on the fake door to the left of the fire-encircled chest to find an eye switch. Shoot it with an arrow. A second floating block appears. Use the longshot on the target above it to land on it, then jump to the next block and step on the switch to get rid of the flames. Drop below and open the chest for the boss key! Exit this room and go through the door to the right.
Avoid the pots that fly at you, then hit the crystal switch beyond the bars (either a spin attack or Biggoron's Sword will do), and go through the door. A Lizalfos will fall from above here, so kill it. There is a sun switch above the door that will make a chest fall, containing bombs, so shine light on the switch if you need bombs. In the next room, kill the bubbles flying around (they look kind of stupid if you ask me), then find the piece of wall that sticks out and bomb it. Turn the mirror so it's shining onto the next mirror, kill the Lizalfos in the next room, and turn THIS mirror to shine through the bars. Go back to the beginning room, avoiding the flying pots. Jump down onto the platform below that is supported by chains (it has light shining onto it) and shine the light on the sun switch to lower the platform.
You're in the room with the big statue. You're close to the end of the dungeon, now. Shine the light onto the statue's face to make it crumble away. Longshot the door to get across, and it will open when you get there. Go through and you meet the two witches, with an Iron Knuckle! The witches leave, letting the Iron Knuckle do their dirty work. Kill the Iron Knuckle as before and... it's Nabooru! The witches don't let her escape... don't let the witches get away with this! Go through the door behind the throne, and climb up onto the central platform to engage with...
In the first stage of the battle, you have to reflect one of the witches' beams (fire or ice) with your Mirror Shield. You have to hold R (don't let go!) and use the control stick to aim the blast at the witch of the opposite power (if you're reflecting ice, hit the fire witch; if you're reflecting fire, hit the ice witch). Continue doing this until the old, ugly witches join together to become a young, attractive (sort of) girl witch.
In this second stage, Twinrova will shoot beams at you, but now the beams don't reflect off your shield immediately. You have to store three of the SAME KIND of beam in your shield until it shoots out. Be warned! If you have absorbed one kind of magic, then try to catch the opposite kind right after, you get hurt! If you've caught ice, sidestep any fire blasts, and vice versa, to avoid this. Stay far away from the elemental blasts if they hit the floor, because they spread out.
Once the elemental energy starts shooting out from your shield, aim it at Twinrova, who will fall onto one of the four pillars. Run over to her and slash her with your sword repeatedly until she gets back up again, then return to the middle platform and repeat the process until she dies. Collect the heart container on one of the small platforms, and step into the light.
After Nabooru does her thing, Rauru will tell you that you need to get yourself down to the Temple of Time to meet someone (?) who is waiting for you there... Before you do that, though, you should collect the last gold skulltulas and pieces of heart.