Immediately upon entry, go to the vines to your left. There are a bunch of Skullwalltulas on that vine, and you can only kill the first few with your Hookshot, so you'll need to climb up the vine slowly to not attract the attention of the other Skullwalltulas. On the 3DS or on other systems, there might be another patch of vines you can climb on the other side of the tree so you don't have to bother with the Skullwalltulas. Once on top of the tree, kill the Skulltula hanging from the ceiling with your Hookshot, then jump across to the other tree and step on the switch. This will reveal a treasure chest with a small key inside.
Jump down and go to the next room. This passageway is full of Skulltulas, but these are no match against your Hookshot. Use your small key to open the locked door at the end and go through it.
Forest Temple, part 1
You're now in the large main room. Go forward and a cutscene will start showing the Poe Sisters taking away the flames, which causes the elevator to lower down. Your job is to regain the flames to re-enable the elevator so you can get to the boss area.
Go straight across to the room in front of you. Here, you'll see a Temple of Time block - play the Song of Time to make it disappear and reveal the door to the next room. In this room you'll have to fight two Wolfos. Kill them and a chest will appear with a small key inside. Return to the main room.
Once back, go to the door to the right. In this passageway, the door will lock behind you and you'll have to fight against a Stalfos. The fight is mainly difficult due to the small size of the passageway, but you can use it to your advantage by simply standing still and striking the Stalfos when he jumps at you (since he cannot walk around he will do this very often) to dispose of him quickly. Once he's gone, the doors will unlock, so continue forward.
You'll now be in a large room with many passageways. This room features a difficult block puzzle where you have to think logically to progress. Continue by climbing the ladders right in front of you. Once up, go around and Navi will notify you of arrows printed on the ground. Ignore them since they're meaningless in Master Quest. Look around the corner and you'll see a green block. Grab it and pull it out so it reveals a path behind it. Follow this path and go right twice and you'll see another green block. Push this one all the way forward and it will sink down which allows you to climb it up. Don't climb it up just yet though as the path is blocked, instead return to where the other block was and climb up the ladder. Here, go around and you'll see a brown block. Pull it back all the way, then return to the green block and climb it up. Now, follow the path there and push the brown block forward which is blocking the path all the way and it will sink as well. Climb it up to the next passageway.
Hitting the crystal switch here will reveal a Hookshot target which is a helpful shortcut for later. Go to the right and you'll find another ladder for you to climb up. Once up you'll be in a room with two Blue Bubbles, ignore them and unlock the door right in front of you to continue. Follow the corridor through and jump down to acquire the Big Key, then fall down the hole right next to you. This room contains a Floormaster, kill it and the door will unlock allowing you to continue.
You'll now be in the second garden area. Follow the path to the right and you will see two doors at the end. Take the right door first and you'll land in a room with a Redead. Kill the Redead and a treasure chest will appear with a small key inside. Once done, go out and take the other door. You'll now be in the block room again, but this time in an isolated part with a crystal switch. Hit it and the corridor at the top will twist. Now, use the platforms and the Hookshot targets to quickly climb up the room and go to the corridor. Go through the now twisted corridor, then jump across the pillars and unlock the door at the end to go through.
You'll now be in one of the Poe Sisters' room, but you can't do a lot just yet so just go down all the way and go into the next room.
You'll come across a room with a large gap in the middle. Don't fall into this gap or you'll have to backtrack all the way. A Stalfos will appear shortly. This fight is similar to the previous fight but because of the larger room, you'll have to change tactics. Block its jump attacks with your shield and strike as its shield is down. (Note that the Stalfos can freely hover over the gap in the middle) Once you kill this Stalfos, a platform will drop down from above and two more Stalfos will appear. You'll have to kill these fast enough before the first Stalfos resurrects. Attack aggressively and use Deku Nuts if you have any to stun the Stalfos. Once these two are gone, a treasure chest will appear in the middle containing the Fairy Bow, which allows you to shoot arrows.
Forest temple, part 2
Go out either door. Here, there are three frames, and in one of them there will be a picture of a Poe Sister. The frame she's in will change periodically. Be careful about getting too close, or else she'll switch which frame she's in. When she's in a frame, shoot the picture with your bow it will disappear. She will now appear in a different frame. Once you've shot all the frames, the Poe Sister will appear and move to the bottom of the room, where you need to fight her. Simply hold your shield out to block her attack, then strike with your sword. Repeat this strategy until she is dead. This will cause one of the flames to appear again in the main room, and it will also cause a treasure chest to appear with the Dungeon Map inside.
Now, go through the door and walk across to the next room. This is just like the previous room - shoot all the pictures, then fight the Poe Sister at the bottom. She's a bit smarter because she likes to skip the attack and just appear out of nowhere. Once she's gone, another flame will appear in the main room, and a treasure chest will appear containing the Compass. You can't go up to the next room because the door is locked, so go all the way back to the main room.
Once there, look at the northeast corridor (the one where the blue flame is). The door is locked, but there's an eye switch above the corridor which you can hit with your bow. Do so to unlock the door and then go through. You'll now be in the first garden area. Go to the right and jump up onto the sides of the well. Look down into the water and you should notice an eye switch, shoot it with your bow to drain the well. Jump down the drained well and open the treasure chest for a small key. There's nothing else to do there, so get back up by climbing the ladder.
Go across the room and you'll see a Temple of Time block above. Play the Song of Time and the block will move a bit closer to you. Now, pull out your Hookshot and look above the door you just came and you'll see a Hookshot target. Use it (you'll probably need to kill the Gold Skulltula first) and once up, jump across to the Temple of Time block. Here, play the Song of Time again and a second block will appear in front of you. Jump across and pull out your bow. Look on the wall at the other side and you'll see a Skullwalltula. Use your bow to kill it, then pull out your Hookshot and pull yourself to the vines, and climb them up to the balcony. The treasure chest here contains another small key. Now, look across to the other balcony and use the Hookshot target to pull yourself over to it, then go through the door.
In this room, first of all kill the Skulltula hanging from the ceiling. Now, you'll notice a door blocked off by a web. While you no longer have Deku Sticks available, you can do something else: stand in front of the torch so you can see the web from it, then shoot an arrow through the torch's flame. The arrow will catch fire and burn down the web allowing you to continue. In the next area, immediately kill the Skulltula doing erratic movements right in front of you. You're now back in the second garden area - just jump down and go through the door at the bottom to return to the main room. Here, take the west door and backtrack all the way to the room where you fought the second Poe sister. Since you now have two small keys you can easily unlock the door at the top.
In this room, jump across to the south corridor and bypass the Green Bubbles (or kill them), then unlock the door in front of you and go through. Here, you'll encounter a small puzzle. Jump onto one of the revolving platforms and jump to the right platform with the frozen eye switch. There will be a wooden box there, pick it up, jump across to the center platform and drop the box onto the switch so the torch will be lit. Now, pull out your bow, and wait until you're perfectly lined up with the torch and the eye switch, then fire a well-placed arrow to melt the ice and activate the eye switch. This will twist the corridor you just went through. Now, destroy the wooden box, then go back through the door. Run through the twisted corridor, then jump down and drop down through the hole.
In the following room, when you run forward the ceiling will drop down on you which will crush you. However, there are holes which allow you to survive. First of all, use your bow to take out all the Skulltulas scattered across the ceiling (there should be seven of them). Then, hug the right wall and run across, staying in the holes when the ceiling drops down. At the end, you'll find a switch, activate it to reveal a treasure chest on the other side of the room. The other switch will unlock the door on the other side of the room. The treasure chest just contains a few arrows and the door in front of you is locked, so run all the way back, go into the passage and open the door there.
You'll appear back in the first garden area. Drop down onto the island to find a treasure chest with a small key inside. To get back, jump onto the first Temple of Time block and play the Song of Time to make a stepping stone appear. Jump up there and play the Song of Time again to make a block appear in front of you, allowing you to get across and return to the ceiling room. To your joy, all the Skulltulas have regenerated so you'll need to kill them all again (or at least the ones on the right side). Then run across the room again and unlock the door this time to go through.
You'll now be in a room with a large Poe Sister painting. Shoot it to start a puzzle. You'll need to push four blocks together to create a picture, which will make the Poe Sister reveal herself. There's also a fifth block, however, which does not belong in there and which you'll have to single out. You only get one minute of time to complete the puzzle so you'll have to be quick. Once the puzzle is completed, the Poe Sister will reveal herself. Just kill her like the other two before to make another flame appear in the main room.
Go through the door, then run across the empty corridor to return to the main room. Jump down to the elevator and the fourth Poe Sister will reveal herself. She works differently from the others - she'll split into four, and only one of them is the real deal. You can easily single her out because the real one will spin around right at the beginning. Shoot her five times with the bow and she will die. Now that all the flames are back, the elevator will reappear as well. Jump onto it and take a ride into the basement.
You can push the walls here to reveal different corridors. Push the walls once counter-clockwise to reveal an corridor leading to a useless treasure chest, it has arrows. Push the walls counter-clockwise again and you'll reveal a corridor with a crystal switch at the top. Shoot the crystal switch to make the bars disappear right behind it, then step on the switch. Push the walls counter-clockwise again to reveal a corridor with two Skulltulas hanging from the ceiling. It has nothing useful, so push the walls counter-clockwise once again to make the path to the boss door appear, but it's inaccessible... Go into the corridor on the opposite side, then turn around and look up to notice an eye switch. Hit it to make the bars disappear which blocked off the path to the boss door. Now, run across and open the boss door...