Kakariko Village After completing the Water Temple, as soon as you enter Kakariko Village, you’ll witness a movie in which Kakariko is in flames. you find Sheik grimly ready to face the boss of the upcoming Shadow Temple, coming out of the well where it was sealed (great place to keep something evil right? In your water supply…)
After getting beat up, you’ll awaken and Sheik will recite more poetry, after which she teaches you the Nocturne of Shadow. Too bad we couldn’t teleport to this town earlier! Would have been nice before. *grumble grumble*
Although we can technically enter the Shadow Temple now, there’s a mini-dungeon we have to tackle beforehand…
~ Getting The Song of Storms ~
Kakariko Village This part isn’t exactly enforced very well, but you would probably have done it on your own if you were curious enough. Most of you probably did it when you got the Hookshot before the Forest Temple.
Enter the Windmill in Kakariko Village and speak with Guru Guru, the furious guy playing his music box. He’ll rant about how some “stupid kid” came here seven years ago and played “that song” which screwed up the windmill. Whip out your Ocarina and he’ll teach it to you. *snicker*
~ Two More Heart Pieces ~
Graveyard Now that we have both the Longshot and the Song of Storms, there’s a host of goodies we can get real quick. First up, head to the Graveyard behind Kakariko Village and pull back the tombstone on the far left, closest to the exit to Kakariko. Drop down to race Dampe one more time.
Dampe’s Amazing Cave Race
We’re back to race again! Follow the ghost of the dead grave keeper and don’t get left behind!
Follow: purple flames, red flames, ghost noises, doors. Avoid: enemies, rupees.
It’s pretty straight forward, for the first chunk, just follow the left wall. After you go through the first door, hug the right wall until you get to the big room, go through the right exit, then take a left and a right (purple flames).
After that door, go along the right side, then when you get to the ledges, climb either the one on the left or straight ahead.
Once you get to the last part, use your Longshot on the torch above to get up there before him, then run through the door at the same time he does. Mwahahah!
By using your Longshot at the end, you should be able to beat him pretty easily, though it may take a few tries. He’ll chuckle and remark on your speed before forking over the Heart Piece. How nice.
Kakariko Village Next up on the list is the man sitting on the blue roof in Kakariko Village. Use the Longshot to get up there and join him, which will amaze him as he gives you another Heart Piece to add to the collection. You can actually get this earlier too by standing on top of the lookout tower and side jumping while holding Z…
~ Last Secret At Hyrule Castle ~ There’s a few more things we can get as a child, so return to the Temple of Time and place the Master Sword back in the pedestal.
Hyrule Castle
Go back to Hyrule Castle and make it past all the guards. You should remember how to do so by now 
Once you get to the end, go stand next to the lone tree in the far corner. Play the Song of Storms to make a hole appear. Completely logical… Fall down it and bomb the wall on your left to find a Gold Skulltula.
~ Froggy Fun ~
Zora’s River Next, go to Zora’s River and go to mid point where there’s logs sticking out of the water. Get on the one closest to “land” and stand on the square mark. Whip out your Ocarina to make frogs appear.
First, play the Song of Storms to instantly be rewarded with a Heart Piece. That was easy. Next, play all of your other, non-teleport songs. For each they’ll reward you with fifty Rupees. Man, these things are so worthless now, especially since most of it goes to waste in your overflowing wallet.
Once they’re all fully grown, whip out your Ocarina again to play a little game. You have to press the button for each frog that has a fly above its head. If you’re too slow or pick the wrong one, you have to start over again. The songs they make you play are somewhat random so you just have to think quick. Once you finally get to the end, they’ll reward you with another Heart Piece.
~ Draining The Well ~ 
Navi will continually harass you now about going in the well, but in the future, it’s blocked off. Return to the past and… well… the well is full of water. I don’t think this part’s very clear, but the windmill draws the water from the well.
Once inside the windmill, go stand before Guru Guru and play the Song of Storms. This will cause it to go haywire just like it did in the future (and also make his reaction to you in the future plausible). The water from the well will drain dramatically, giving you access to the next mini-dungeon. Sweet.
Go back outside, climb down it and head on through.
~ Within The Well ~
Entry As soon as you enter, crawl through the hole then go down the ladder. A big Skulltula will block your path. He should be easy enough for you to defeat, but now your sword isn’t as long as you’re used to. After he’s defeated, check out the skeleton nearby if you like… There are several parts in this game where it’s not very clear what you have to do. This is one of those moments.
The entire dungeon is filled with fake walls. That being said, walk through the wall straight ahead, besides the skeleton.
Main Room
This whole room is shaped like a doughnut, with a hidden room in the middle. For right now, work your way to the opposite side, being careful for the invisible Skulltulas along the edges of the walls and the giant Green Bubble that circles through the area counter-clockwise. The latter you can only kill when its flames occasionally go out.
Anyway, like I said, go to the opposite side (follow the source of the water). I suggest killing the Green Bubble, then taking the right side. Once you get there, you’ll find a weird stone imp head sticking out of the wall with water flowing out its mouth. Play Zelda’s Lullaby on the Triforce symbol on the ground to stop the water flow.
~ Getting The Lens of Truth ~ 
Return to the beginning of this room where you walked through the invisible wall. Now that the water is gone, you can jump down into the pit. Open the small chest if you like, it just has Bombs. Crawl through the small hole.
Watch out for the Skulltula hanging from the ceiling. After killing it, climb up the vines and go through the door.
Dead Hand Room Ack! Here you’ll find a creepy new enemy called Dead Hand. Let one of the hands grab you, then mash the A and B buttons to get free. Wait for the body to get close and smack the head once it’s about to bite you. Repeat. While creepy and intimidating, he’s not that hard.
Once he’s defeated, open the large chest that appears to find the Lens of Truth. Go back to the previous room.
~ Basement (Dungeon Map) ~
Return to the previous room. Kill the Skulltula, which conveniently has its back faced to you. Crawl back through to the main room. Now, honestly we have everything we need from this dungeon, so you can leave right now if you wish. The rest of the mini-dungeon is just to get Skulltulas. That being said, onward, for glory!
Main Room First off, you’ll notice there’s lots of pits that lead to the basement of this dungeon. Because you’ll most likely fall in one accidentally if this is your first time, I’m going to cover that first. If you wish to fall down intentionally, the hole in the very middle of the main room (directly beneath the “X” shaped poles) is the best way.
Basement
This large cavern splits into four paths that all lead to dead ends. The one on the far right (with the two burning torches) leads to the Dungeon Map. use Bombs on the two boulders blocking the way, then use the Sun’s Song to stun the ReDead. Kinda scary to see those things in the past, no?
After snagging the map, go back to the pit of despair. It would be good to kill the ReDead beside the poison water. After that, snag the three Silver Rupees near the planks and go up the ladder. Snag the Rupee here and go up the second ladder. Collect the final Silver Rupee to open the door. Go through and it’ll close behind you.
Anyway, if you fall down at any point again, that’s how to get out.
~ Getting The Compass ~
Main Room If you go to the center… room… inside the main room, you’ll see a large chest in one of the fenced in alcoves. Using your Lens of Truth, you can see there’s a pit blocking the entrance though. Don’t try jumping across, it won’t work. Just look around inside that alcove and you’ll notice one of the side walls is fake. Walk around the outside and go in to snatch the Compass. Go back the safe way now 😉
~ Coffins ~
Main Room
Now, it’s time to round up some Small Keys. We’ll tackle the oddball one first. On the west side of the dungeon is a pit with metal grating over it, which was filled with water before. Jump down and open the small chest if you like, the climb the vines and go through the door.
Coffin Room As you enter this room filled with traps, you should kill the Gibdo first. Use the Sun’s Song to stun it first, makes it a lot easier.
After that, we need to open the coffins by lighting to torches beside them using Deku Sticks. There’s enemies inside them, along with goodies. The casket in the southwest corner of the room (opposite the door you entered from) has the Small Key in it. Return to the main room.
~ Small Keys ~
Main Room
Now, you’ll see on your map that there are two chests hidden in each corner of the southern part of the main room, within the walls. If you walk around there using the Lens of Truth, you’ll see little alcoves with chests.
Open them both to get two Small Keys.
~ The Two Rooms ~
Main Room In the center of the main room is two small rooms we’ve ignored thus far. Inside each of their locked doors is a Skulltula.
Skulltula Room – Left
There’s simply a lone Deku Baba in here… and some killer porcelain. I suggest using your shield to run forward and deflecting the projectiles before assaulting the plant. Snag your prize and head to the other room.
Skulltula Room – Right This one’s a little more complicated. Stay on the ledge and kill the many Keese from a distance. After that, use your Lens of Truth to see the invisible walkway to the other side so you can claim your prize.
~ Last Skulltula ~
Main Room
In the northeast corner of the main room is a small hole you can crawl through. Do so to find a locked door. Use your last Small Key on it.
Pit Room This room is filled with viceous pits and several Fire Keese. First equip your Hylian Shield so they don’t burn your other shield, then use the Lens of Truth to get closer. It’s easiest to simply let the Keese hit your shield, then slash them to defeat them.
Using the Lens of Truth, throw a Bomb at the Beamos to kill it. If you lost your Deku Shield to the Fire Keese, the small chest in the corner contains one. Maneuver to the other side and go through the door.
Like Like Cage It can be hard to move around in this small room and the Like Like will probably eat you at least once. I suggest circling around it, Z targeting and stabbing it quickly, jump back, repeat.
Once it’s defeated, open the chest for either type of shield should it digest it, then snag the Skulltula token. Yipee!
And that’s it! Make your way out of the dungeon. There’s more goodies here really, but it’s all items like Bombs, Bombachus and Deku Nuts…
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