The Shadow Temple is the seventh dungeon of the game, and a very weird one at that. There are plenty of fake walls, guillotines, invisible spikes, and other fun things like that. You'll need the Lens of Truth and the Longshot to complete it.
Entering the Temple
To get to the Shadow Temple, you must have completed the Water Temple, and also the Bottom of the Well mini-dungeon. After completing the Water Temple, go to Kakariko Village, and witness a cutscene in which a mysterious monster breaks loose from the Well. Sheik will then teach you the Nocturne of Shadow. To complete the Bottom of the Well mini-dungeon, you must obtain the Song of Storms in the Windmill as an adult, then return to the past and use it to drain the well, allowing access to Bottom of the Well.
After you do this and obtain the Lens of Truth, play the Nocturne of Shadow as an adult to warp to a ledge in Kakariko Graveyard. You can only get to this ledge by use of the warp song, but you can then get back down into the Graveyard, making this a helpful warp song even if you aren't going to the Temple. Anyway, go down the passage in the wall, stand on the platform, and use Din's Fire to light the torches, opening the gate to The Shadow Temple.
Getting the Hover Boots
Once inside the temple, run forward until the wall, then pull out your Longshot and look to the right to see a Hookshot target. Latch yourself onto it to safely get across the pit, then continue by walking through the face.
In this room, there is a statue and multiple skulls. By using the Lens of Truth, you'll see that only one of the skulls is real, and the others are all fakes. You need to push the statue so it faces the real skull. If you fail, a trapdoor will open beneath your feet, but if you succeed, the path to the next part will open. The only problem is that you can't get over there... To solve that, look at the statue over where the grating is and you should notice two torches at the hands. Light them up with Fire Arrows and a platform will appear so you can get across. Follow the path down to the next room which appears to be a dead end with a Beamos, but try to go through the right rock wall and it turns out to be fake. Open the door behind it.
In this room you'll have to fight two Gibdos. Simply use the Sun's Song to stun them, then attack them one by one. Once they're dead, a treasure chest will appear containing a small key. Now return, and this time walk through the rock wall straight ahead and open the door. Here, you have to collect five silver rupees, which is made difficult by the spinning scythe. The two silver rupees in the middle can be collected by waiting until the scythe passes you, then quickly running to it and afterwards running to the wall. The third silver rupee in mid-air can be collected using the nearby Hookshot target and jumping off to collect it. Kill the Skulltula guarding the left alcove and get inside to claim another silver rupee. The last silver rupee is guarded by another Skulltula. Once all five silver rupees are collected, the grating will disappear allowing you to go through. Inside, kill the Skulltula there and open the chest to claim the Dungeon Map.
Now, return all the way to the first room with the bird statue. Strike your sword at all the faces at the wall, one of them should make a hollow noise. Plant a bomb there to destroy the wall, and then go through and unlock the door. In here, there are loads of fake walls. You could of course just use the Lens of Truth, but an easier way is to look at the eyes of the drawing (fake walls have glowing eyes). Go right and to the first door you encounter. Inside, there are four Redeads for you to kill. Use the Sun's Song to stun them, then strike. (You could just use Din's Fire for an easy kill) This will cause a treasure chest to appear containing the Compass.
Go outside, and go to your right. At one spot at the wall Navi will glow green, here play the Song of Time to make a Temple of Time block disappear allowing you to go through. On the other side, there are three eye switches to your left. Only the middle one is real (the two others are enemies), so shoot it. Then go into the northwest corner, pass through the fake wall and open the door....
Miniboss: Dead Hand
This battle with Dead Hand is exactly the same as it was in the Bottom of the Well mini-dungeon, but now you have an advantage: the Lens of Truth. If you use it, you will see a very obvious dark shadow on the ground. That signifies where Dead Hand is hiding. Go to the hand farthest from that point, and get captured by it. Then, quickly struggle to break free, then attack Dead Hand when he lowers his face. You can only get in one hit, so make it a jump attack. Two jump attacks from the Biggoron's Sword (which you should have by now, otherwise, check out the Trading Sequence. Once you kill him, a Treasure Chest will appear. Open it, and obtain the Hover Boots. These boots are similar to the Iron Boots (i.e. they function as items in the 3DS version, but as upgrades in any other version, and are a pain to put on). However, instead of weighing you down, they instead allow you to briefly walk on thin air (don't ask me how that works). As a downside, though, they have no traction. Also, a cool trick with them is that you can walk over invisible crystal spikes without getting hurt!
Delving Deeper into the Dungeon
Now, return to the room with the single Beamos. Walk through the left wall to return to the scythe room. This time, get to the alcove with a face at the wall. It will tell you to come over if you want a "ferry to another world". Approach it and you'll fall through an invisible hole. You are actually now much deeper in the dungeon, however, a large block is stopping you from continuing. Kill the invisible Skulltula near the brown block with the Longshot. There's also an invisible treasure chest here, open it for a small key, then return to the room with the Beamos. Plant a bomb at the east rock wall to blow it up, then unlock the door and go through. Go down the passageway, but be careful because there's a Beamos just around the corner. Kill it with bombs, then continue through the floor spikes, behind them a Skulltula will come down from the ceiling so kill it.
At the bottom you'll see two guillotines and a Beamos. Jump down, then first throw bombs at the Beamos to kill it (the bombs pass freely through the guillotine so don't worry), then run across when the blades are moving up. Continue and you'll be in a large area. The first guillotine moves very fast and so is very tricky to pass. Pass through it, jump down and you'll see two Beamos on the other side, kill them by shooting arrows at the bombflower. Just as you approach to jump, a Red Bubble will pop out so be careful.
Once at the bomb flower, walk to your left and pull out your Lens of Truth - there are invisible platforms here. Jump on the first one, then look down to notice a frozen eye switch, use a Fire Arrow to unfreeze it (you first need to disable the Lens of Truth because otherwise it won't work). Jump onto the next invisible platform and open the door at the end. Follow the path, and at the end kill the Like-Like first. You need to collect five silver rupees here, but there are ten silver rupees here - some are simply fake. Collect all of the ones in the middle and then get to the corner where the last one is. Play the Song of Time and a Temple of Time block will appear allowing you to get the last one, which opens the grating. Inside, the visible chest just contains a Blue Rupee, but there's an invisible chest just next to it which contains a small key. Now, return to the beginning area.
Return to the platform with the bomb flower. Cross the ice platforms until you come to another area. There are five silver rupees them, but ignore them (you get arrows if you were to collect them) and instead get to the grating on the other side. Slash the crystal switch behind the grating to open it, then go through the passageway. In the next area, look to the right with your Lens of Truth to notice a brown block. Pull it out, then push it all the way forward to safely pass through the area. At the end, there's some higher ground that allows you to climb on top of the brown block - do so, then get to the other side and step on the switch there. This makes a treasure chest appear with a small key inside. (The other treasure chest here contains a Blue Rupee, and the chest at the bottom in the northern cell contains arrows.)
Return to the room with the Beamos and the spinning spikes. Walk on the narrow path and get to the guillotine where the sign stands. Behind the guillotine there are invisible platforms, so just jump across. Get onto the moving platform, then equip the Hover Boots and run across to the locked door, unlock and open it. Inside, there are Redeads, stun and kill them and a treasure chest will appear (it contains a blue rupee). Now, collect the silver rupees on the floor, but watch out - there are invisible spikes scattered across the room, and they hurt Link if he tries to walk over them. At the walls are Hookshot targets which you can use to collect two more silver rupees. Look at the ceiling to see two more Hookshot targets which again can be used to collect silver rupees. Now, while the remaining silver rupees look impossible to collect, look around with the Lens of Truth to notice invisible Hookshot targets which can be used to collect these. Use the Hover Boots to get the last one and the doors will unlock.
Open the locked door. Look around the corner to see fans. Run across when the wind isn't blowing (watch out for the Skulltula on the way). At the end, there's a gap, but you can use your Longshot to latch yourself onto the wooden bar to get across. At the end, there's fans blowing from the side, use your Iron Boots here to safely get across and open the door at the end. Inside there are four Redeads, play the Sun's Song to stun them and then kill them. Afterwards open the invisible chest in the corner to get the small key, then exit the room.
The Ghostly Ship
Use the Lens of Truth to notice a hidden passage to the right. Equip the Hover Boots and run there when the fan is blowing so it pushes you across, once there open the door. As always, stun and kill the two Gibdos here (you'll get a blue rupee for your efforts), then continue through the locked door. Does this room look familiar? Its the same one that we went down to get a small key, but a brown block stopped us from going any further. Pull that same brown block into the depression so it sinks down, and now you have a shortcut to the upper floor (however ,whatever you do, don't go to the upper room before you have pulled the block as far as it can go, otherwise you will be unable to return). You can now jump on the block, climb up the ladder and get on the ship. On the large Triforce symbol play Zelda's Lullaby which causes the ship to start moving. Your voyage will be accompanied by some Stalfos, kill them or wait until they fall off the ship on their own. At the end when you see solid ground to your left, jump off as the ship will sink soon.
Across the pit you'll see a bunch of bomb flowers. Shoot them with an arrow to make the bird statue fall down, creating a bridge. Cross the bridge, then walk to your right to see a Temple of Time block next to a gray block. Play the Song of Time to make the Temple of Time block disappear, which will uncover an eye switch. Hit it to make some Hookshot platforms appear. Jump onto the one right next to you, then look up to notice another Hookshot platform up high. Latch yourself on it and step on the switch there to unlock the door. Cross the bridge again and walk through the door at the west.
The Boss Key
This room looks completely empty at first, but use your Lens of Truth to notice it's actually a large maze. Walk to the north, then go around the corner and kill the Like-Like there, afterwards continue going to the west door and enter it. Ignore the vases, but run behind them and collect the small key lying on the ground. Go back into the maze, and this time make your way to the north door, unlock and enter it.
Here, there are two wooden spike walls that move together to crush you. Use Din's Fire to burn them down, then quickly kill all the Fire Keese that have now turned up. Afterwards open the treasure chest to the right to collect the Big Key (watch out for the invisible Skulltula). The other treasure chest just contains a blue rupee. Return to the invisible maze room, and if you need more arrows, take the south door (it isn't actually necessary)
Won't this guy die already?
If you did enter the south room to get more arrows (which you will need for the dungeon boss), you will notice a bunch of Bomb Flowers. Also, if you use the Lens of Truth, you will see a dark shadow on the ground, like when you fought Dead Hand.
This battle with Dead Hand is easier than the others. Just look for him with the Lens of Truth, shoot an arrow at the nearest Bomb Flower, and then he will arise. When he lowers his face, jump attack him. Repeat. He will quickly die, and a chest will appear, containing... arrows. Rather useless. However, you will need them (a lot of them) for the final boss battle in this dungeon.
To the Boss
Return to the bird statue room (take the east exit in the maze) and unlock and open the south door on the other side this time. Here, there are multiple invisible platforms, use your Lens of Truth to see them and walk across to the boss door and open it. (Note: the more fairies you have with you, the better. Bongo Bongo might kill you multiple times before you vanquish him. Also, make sure that you have plenty of magic power)
Phantom Shadow Beast: Bongo Bongo
You find yourself in a room with a hole in the center, similar to King Dodongo's boss room. There's nothing else to do here but jump down...
You will fall down (don't worry, you won't take damage), and find yourself on a large, circular white surface, surrounded by a pool of poisonous liquid (hint: don't go into that pool). A disembodied pair of hands will begin drumming on the surface (which is a drum, presumably a bongo), and then a creepy floating, one-eyed body will appear, the boss music will play, and: Phantom Shadow Beast: Bongo Bongo
Bongo Bongo's main body will immediately disappear, but his hands will remain. There are two strategies for defeating Bongo Bongo, with Ice Arrows or without. However, either way, DON'T USE THE HOVER BOOTS! You might think that the dungeon item would help defeat the dungeon boss, but that just isn't so. The only items you will need are the Lens of Truth and the Fairy Bow (and, of course, your trusty sword).
Without Ice Arrows
This is the strategy if you don't have the optional Ice Arrows from the Gerudo Training Grounds (you can actually get them before beating the Shadow and Spirit Temples).
What you have to do is shoot each of Bongo Bongo's hands so that they are both stunned at the same time. This is actually much harder than it sounds, for two reasons. First of all, Bongo Bongo is constantly drumming, so it's often very hard to actually hit one of his hands. Secondly, if you take too long, Bongo Bongo will grab, smack, or other wise attack you. If he grabs you, he will suck out life energy like a ReDead, and possibly throw you into the poisonous liquid. Once you have stunned both hands, use the Lens of Truth, to see that Bongo Bongo is preparing to rush at you. Shoot him with the Bow, and then slash at him with your sword (jump attacks work best, especially from the Biggoron's Sword). After a couple rounds, he will die.
With Ice Arrows
This is the strategy if you have the optional Ice Arrows from the Gerudo Training Grounds (you can actually get them before beating the Shadow and Spirit Temples).
The Ice Arrows make this battle much easier, however, some caveats. You cannot shoot a magical arrow (Fire, Ice, or Light) while the Lens of Truth is active. So, when you are shooting Bongo Bongo's eye, you will have to switch to regular arrows. Also, it's still equally hard to actually hit Bongo Bongo's hands; the Ice Arrows don't change that.
With the Ice Arrows, you only have to shoot one of Bongo Bongo's hands. It will freeze, and then the other one will hammer at it and try to break it, effectively incapacitating both of them! Now, switch the regular arrows. Activate the Lens of Truth so that you can target Bongo Bongo's eye (just make sure that neither of the hands are in the way of your arrows). Shoot his eye with the Arrow, and he will crash to the ground, vulnerably to the sword. Repeatedly hit him with jump attacks (preferably from the Biggoron's Sword). After a couple rounds, he will die.
Bongo Bongo's Death
After you defeat him, Bongo Bongo will become a dark puddle on the drum, and then evaporate. Congratulations! You just beat possibly the hardest boss in the game! Don't forget to grab the Heart Container, then warp out. Impa will tell you that she is the Sage of Shadow, and that Princess Zelda is safe. Then, you get the Shadow Medallion. On to the Spirit Temple!