Get the Map
Bomb the two cracked blocks at the upper left of the room. You can bomb the upper left block by placing it in the corner near it. Then push the middle block left. Exit to the west.
Kill the Pols Voices by throwing a bomb at them. You can either try to back it into a corner and throw the bomb, or hold onto a bomb until it starts flashing, then throw it.
Open the chest that appears to get the Dungeon Map.
Break the First Crystal
Go back to the dungeon entrance. If you're to the left of the blocks in the northwest corner, bomb the upper block and push the upper-right block to the right. Then exit to the north.
In the room with the two Moldorms, the upper door is locked, so kill the Moldorms and exit to the east.
The iron masks in here can't be hurt from the front, so try to get around to the back and hit them from behind. The owl statue here says that the four crystals tie it all together. One of these crystals is in this very room. Break it with your sword and you will hear a distant sound.
Break the Second Crystal
Go north and go into the turnstile. This revolving device will move you to the right side of the room. It will switch direction, so if you get back in, you will go back to the south side of the room. Exit to the east.
Use a bomb to crack the block near the statues on the right side of the room. Then stand next to the short wall and throw it over to where the crystal and cracked rock is. Then go up to the upper-left short wall. There is a block to the right of it that you can push down. Once you do, stand at the short wall and throw a bomb to where the crystal and cracked block is. Then go down to the bottom of the room and push up the block that is southwest of the crystal. Now you can go up to the crystal and break it with your sword.
Get a Key
Now go to the block to the right of where the crystal was and push it up. Then push the statue to the right twice, up twice, left once, and down once. This makes a small key fall from the ceiling.
Break the Third Crystal
Go back to the last room and use the rotating device, then go south, then west. Use your new key on the door in the north wall and go through.
In this room, there are peahats, and a big hole in the floor between some statues. Don't bother exiting to the east because it will just take you to the rotating device, which will just put you back into the room with the first crystal. You can't push the blocks to reach the left side of the room and you can't open the door above, so just fall down into the hole.
A bunch of tektites and zols will attack you, so be ready to fight them off. There is only a dead end to the east, and you won't be able to do anything in the room to the north, so use the south exit.
Use a bomb or just your sword to kill the moldorm in the closed area. Once it's gone, you can exit to the south.
Use bombs to kill the Pols Voices in the closed area. Try holding the bomb for a moment before throwing it, but don't hold it too long. Once you kill the Pols Voices, the north door in the middle will open. Go through it.
Go to the left, then exit north to reach some stairs. Go up. Break the crystal.
Get the Compass
Go back down the stairs. Go south to the room with the moldorm in the closed area. Use a bomb to kill it, then go through the south door on the left that was opened.
Follow the path to a room with a conveyor belt and a crystal switch. Throw a bomb onto the conveyor belt such that it explodes near the crystal switch, activating it. The armos statue will come to life and start walking around. Throw a bomb at it to kill it. Then open the chest to get the Compass.
Get a Second Key
After getting the compass, go up the stairs at the upper-left that you couldn't reach before you killed the armos statue.
In the room where you can see the Pols Voices down below, go south and exit to the west.
You need to make the upper blocks match the pattern of the lower blocks to make a diamond shape. Push the upper middle block up, the upper left block left, and the upper right block right. Get the key that falls.
Get a Third Key
Go back to the last screen and go down the stairs. Then go east, north and use the northwest exit to reach the stairs. Go up.
Push the rightmost block to the right, then exit east. Use the rotating device and exit to the south. Then exit west, north and east to use the rotating device again. This time it's going in the other direction, so you will be able to exit to the north.
Beware of the Like Likes here. These worms will eat your shield if you get too close, so try getting rid of them by throwing bombs.
Ignore the crystal up above for now and exit to the east. Step on the switch in the top right corner to bring the statues to life. They can be killed with Scent Seeds. If you don't have scent seeds, bombs also work, but it's difficult to get the bomb to explode before the statues walk out of the way. When you kill all of the armos statues, a key falls from the ceiling.
Get 30 Rupees
Go back to the last room and unlock the upper door with a key.
In the next room, use your sword or shield to block the flying tiles that hit you. Try to get rid of the Zols and Gels as soon as possible. The doors will open after the tiles are all gone. Exit to the left.
One of the bushes in here hides a spiny beetle, so be careful. Exit to the south.
Go around the room, being careful of spiny beetles hidden in the bushes, and use the northwest exit.
There are more spiny beetles in the bushes here. Go up the stairs and exit to the south. Get the 30 rupees from the chest and go back north.
Get the Seed Shooter
Use your key to unlock the door in the northwest wall and go through.
You can't do anything with the torch in this room, so just exit to the west.
Kill the Moldorm and the Arm Mimics. The mimics will walk when Link walks, going in the opposite direction from the way that Link is going. Use this to your advantage to make the mimics come to you. Once you have killed all of the enemies in here, open the chest to get the Seed Shooter. This item allows you to shoot seeds like bullets.
Break the Fourth Crystal
Go back to the last room and use an Ember Seed with your seed shooter to light the torch in the middle of the room. Exit to the south.
Go up the stairs and drop down to the east, then exit to the east. Wait for all of the tiles to be gone, and get rid of the Zols, and the doors will open. Exit to the south.
Equip your seed shooter, stand at the short wall near the crystal, and hold down the button for the seed shooter. Use the control pad to make Link aim diagonally at the crystal, then let go of the seed shooter button. This will break the fourth and final crystal.
Get a Gasha Seed
Exit to the south to find a treasure chest that contains a Gasha Seed. You can now walk in any direction in this room without having to use the rotating device.
Get another Gasha Seed
Exit to the left and fall down the hole. Exit to the east and use the rotating device, which has fallen down to this floor. Then exit to the south.
Kill the two iron masks. The blocks on the right side of the hole can be pushed into the hole, so do that. Then use the seed shooter to light the torches with ember seeds. The seeds will bounce if they hit a wall. Experiment with places to stand to figure out how to hit the two torches. Here is an example:
2** *** BTBTB *1*
The letter T above represents the two torches. B represents the blocks around the torches. The * are the tiles to the right of the gap with the torches. Stand on 1 and aim northwest, and stand on 2 and aim southwest.
When you light both torches, a chest appears that contains a Gasha Seed.
Reach the Mini-Boss
Exit to the west, then exit to the north, and finally, use the east exit. Use the revolving device to exit to the north.
Go past the peahats to exit to the north.
To defeat Subterror, use your shovel to dig it out of the ground, then attack it with your sword. Be careful because he crawls around after you dig him up. He starts moving more quickly as the battle progresses and it becomes harder to dig him up. If you take too long, he will drill up from the ground to attack.
Get a Fourth Key
After you defeat Subterror, exit to the west, then exit to the north. Kill the Moldorms by swinging your sword over the blocks, and then push the bottom-right block to the left (you won't be able to push it until the moldorms are gone.) Get the key that falls.
Get 20 Rupees
Go back to the revolving device and exit west. Then use the north exit.
Hit the crystal switch to make it rotate the item in the top middle of the area. Then use the seed shooter on the rotating item to hit the switch in the middle of the room. The grass here will regrow, so you can use it to keep replenishing your seeds if necessary. On the other side of the bridge, hit this crystal switch and hit the bridge switch again to reach the chest down below that contains 20 rupees.
Get the Boss Key
Unlock the door in the top right and go through.
Use the seed shooter to hit the crystal switch across the way, then hit the rotating item to hit the switch in the middle of the room.
After crossing the bridge, use the crystal switch to rotate the item so that you can hit it with the seed shooter to hit the switch in the middle of the room. Exit to the north.
Since you don't have the Boss Key, push the block on the right to the right, then make your way back to the revolving device. It will be pointing in the direction that you couldn't go before. Exit east.
Step on the switch so that the rotating items have a space between them that points diagonally toward the switch down below. Then shoot your seed shooter at the upper wall at an angle. It should bounce on the upper wall, the right wall, and then should pass through the two rotating things and hit the switch. Exit to the north.
Get the Boss Key from the chest and drop down. Go west, then north, then follow the path to the boss door room, where the block that you pushed earlier is still where you left it, so you can go through.
Shadow Hag's shadow will split apart and attack you. Stay away from the shadows. Eventually the shadows will reconvene and turn into a small shadow with eyes. This shadow will spit out some moths. Kill the moths, and then don't move. Shadow Hag will appear behind you. Don't turn around or move, because Shadow Hag will disappear. Instead, use the seed shooter at the wall to make it bounce off and hit Shadow Hag. After doing this several times, Shadow Hag will die.
Get the Essence
Go west to get the Echoing Howl.
You'll see a cut scene showing that the Black Tower is almost finished. The Maku Tree will tell you that there is an essence in the mountains northwest of Lynna City. Your next stop is Symmetry City.