After getting the Hookshot from Dampé in the Kakariko Graveyard, you can reach the entrance to the Forest Temple in the Sacred Forest Meadow where you learned Saria's Song in the past.
Get a Gold Skulltula
Two wolfos attack. Fight each one one at a time. Before moving on, hookshot the vines to the right of the right-hand tree and climb up. Hookshot the gold skulltula up here.
Get a Key
Go to the end of the branch and hookshot the chest on the other tree. Open it to get a small key. Drop down below and go through the door.
Get a Second Gold Skulltula
Kill the skulltula with the hookshot. Its whole body is vulnerable to the hookshot. Go through the door.
Go toward the center of the room. After the brief cut scene, go straight across the room. Before leaving, get the gold skulltula on the wall to the right of the stairs. Then go through the door up the stairs.
Get a Second Key
To kill the blue bubble, raise your shield and walk into it to remove the flames, then kill it with your sword. Go through the door.
Two Stalfos will attack you. Target one of them, and if it is close to you, try moving around it and attacking its side with your sword. If it gets close and then jumps back, move to the side to avoid its jump attack. After it jumps, hit it. After you kill them both, get the small key from the chest. There is a fairy in one of the jars in this room. Return to the big central room.
Get the Map
In the arch in the northwest corner of the room (to the right of where you came from just now), there is a Song of Time block. Play the Song of Time to make it disappear and reveal a door. Go through.
Kill the Deku Baba and Octorok. Go to the vine wall and kill the two skulltulas that you can hit with your hookshot, then climb up and stay far to the right to avoid the skulltula up above. Climb up to the ledge and go through the door.
Kill the blue bubble and open the chest to get the dungeon map. Then exit through the door below the swirly symbol.
Empty the Well
Use the hookshot on the target on the opposite wall to reach the ledge. Step on the switch to empty the well. Go down to the grass.
Get a Third Gold Skulltula
Use the hookshot on the front of the small chest on a ledge. You will reach the ledge and be able to kill the gold skulltula here.
Get a Third Key
Go down the ladder in the well. Open the chest to get a small key.
Get the Fairy Bow
Climb up the vines at the end of the well passage where you opened the chest. Go through the door near the Deku Baba to reach the large central room where the ghosts took away the fire.
Go through the locked door above the ledge and stairs on the side of the room. Kill the skulltula in here and go to the next room.
Kill the blue bubble and climb up the ladders straight ahead. Find the big block and push it along the arrows on the floor. Then use a nearby corridor to go to the other side of the block and push it that way. Eventually the block will slide into place on the floor.
Go back to where you first found that big block. Climb up the ladder there. On this third level, there is a red block. Push it until it stops. Go back down to the other block and climb on top of it. From here, you can reach another side of the red block and push it until it slides into place. Climb up.
In the next area, kill or ignore the blue bubbles, then go through the locked door.
Go through the twisted corridor. When you reach the small room at the end, jump down to the bottom. You will hear a sound and see a shadow over you. Run in circles to prevent the Wallmaster from landing on you. When it lands, kill it with your sword. If it lands on you, it will take you back to the beginning of the dungeon. Climb up the ladder and go through the locked door in this room.
There is nothing to do in this room yet, so just go down the stairs and go through the door.
Stalfos will attack. Be careful not to fall down below. After you kill the first Stalfos, a couple of others will appear. If you kill the first one but take too long fighting the second one, the first one will come back to life.
After killing the Stalfos, you get the Fairy Bow.
Get the Compass
Exit through the door with the blue carpet. You will be back in the room with the stairs and the paintings of Poes on the walls. You have to shoot each painting with an arrow while the ghost is visible. If the ghost disappears, walk away from the painting and wait. Once you shoot all of the paintings, the Poe will come to life and float down to the bottom of the room. Follow it, but keep your distance, and shoot it with an arrow when it appears. After you kill it, you get the compass.
Get a Fourth Key
Go through the door next to where the ghost's flame lit the torch. This is where you fought the Stalfos to get the bow. Go through the door across the room. There are paintings in this room as well. Shoot the poe paintings and kill the poe to get a small key.
Get the Big Key
Go up the stairs and go through the exit. Go through the twisted corridor and go into the room with the blue bubbles. Shoot the eye switch on the wall to untwist the corridor. Go through the corridor and into the room at the end. Drop down to the lower level and kill the wallmaster like you did before. Open the chest to get the Big Key, then drop into the hole in the floor.
Get a Fourth Gold Skulltula
Kill the two bubbles and go outside to the west courtyard. Jump to the narrow walkway and get the gold skulltula on the wall at the end.
Get a Fourth Key
Carefully jump back to the ledge that you came from, and kill the deku baba on the way. Go into the room on the right. A floormaster is here. Sometimes it turns green and tries to punch you, so raise your shield or sidestep it. You can stun it with the hookshot. Once you kill it, three small hands appear. If you are not quick to kill them, the small hands will grow into large ones. These enemies always drop magic jars, so feel free to use Din's Fire. When you have killed the floormaster, get the small key and exit.
Open the Elevator
After leaving the floormaster room, exit through the door on the right.
Drop down, then turn right and go up the ladders. Once you get up to the level with the red block, go through an arch to find yourself at a ledge with a fence on it. Hit the gold eye switch on the wall with an arrow to make a chest drop down that contains arrows.
Climb up to the area with the blue bubbles and the eye switch just before the twisted corridor. Shoot the eye to re-twist it, and go through. Jump over the ledges and go through the door to reach one of the rooms where you fought a ghost. Go down to the bottom and go through the room where you fought the Stalfos. You will reach the other room where you fought a ghost. Go up the stairs, then unlock the door and go through.
Drop down to the floor and run in circles to avoid the wallmaster. Kill it, then climb up to the other door. Kill the green bubbles and go through the locked door.
Jump onto one of the spinning platforms and get an arrow ready. To activate the frozen switch, you must shoot your arrow through the flame and hit the switch with the burning arrow. Once you have done it, the corridor will twist. Go back to the corridor. Kill the green bubbles and go to the room at the end. Jump down the hole on the bottom floor.
In this room, watch the falling ceiling to find the safe spots that you can stand in when it falls. Avoid tiles that have shadows over them, because a skulltula is hiding there. The first safe hole is to the left. Next, run to the switch on the right and step on it. It's on a tile against the right wall. Finally, run to the left side of the chest (there is a safe tile to the left of the tile that the chest is on) and open it. Run to the exit and leave the room.
When you shoot the poe painting in this room, a block puzzle falls from the ceiling. Be sure to pay attention when the camera shows the puzzle from above. One of the blocks is blue and the others are green. The blue block is the one wrong block that doesn't belong in the picture. There are four that do belong. Here is a diagram looking down from above. The wrong block is marked by an X.
O O X O O
Pull the wrong block away from the rest of the puzzle, and push the remaining blocks into place. If you don't do it in time, the blocks shuffle, and the wrong block is in a different place. When you successfully put the puzzle together, a poe will attack. Shoot at it when it is not invisible. After you kill it, go through the door that opened.
Kill the skulltula and go to the next room.
The final poe is in the middle of the central room. Go to the center and the poe will split into four copies. The real copy is the one that spins after it splits into four. Quickly target that one and shoot it. Try moving to a corner of the room where there is more space. Keep shooting the poe that spins. The elevator will rise. Get into it to go down to the lower floor.
Get a Fifth Gold Skulltula
You can rotate this room by pushing one of the large slabs sticking out of the wall. Try to always push in the same direction to avoid getting confused. Rotate the room and then check both doors each time. You must step on the three switches in this room to open the gate. There is also a gold skulltula in the room with a regular skulltula.
Reach the Dungeon Boss
After stepping on the three switches hidden in the rotating room, look for the door that you can open with the Boss Key. It's in a tunnel with a blue carpet. Go through the Boss Door.
To start the battle, walk to the center of the platform, then try to go back out the way you came. Bars will appear, blocking your exit. Stand on one of the small Triforce symbols around the perimiter of the platform. Get an arrow ready to shoot, and watch the paintings for a horse to approach. If the horse turns around, then you're looking at the wrong horse, so look around the room for the real horse to come out of the painting surrounded by purple light. Shoot that horse with an arrow. You're safe even if you miss, because Phantom Ganon's lightning can't hit you if you're on one of the Triforce symbols on the edge of the platform.
Keep shooting at the horse until Phantom Ganon comes out of the painting and starts floating around. When he shoots a ball of energy at you, hit it back with your sword. Don't wait too long before swinging your sword, or you'll get hit by the energy. Don't swing your sword too soon or you'll miss and get hit. Keep hitting the energy back and forth with Phantom Ganon until the energy hits him and he falls to the floor. Run up to him and attack repeatedly with your sword. Repeat the process until the phantom dies.
Now you have the Forest Medallion. Your next stop is Goron City.