IT WAS A DARK AND STORMY TEMPLE....
Enter the temple and cross the chasm with the Longshot. You'll come to a fake dead-end, so step through the wall with the face on it. In this room, use the Lens of Truth to find a passage going through another one of the smiley-face pictures in the wall. Proceed down this passage, and there are two other fake walls. Down one passage is a room with bats and Gibdos, which when all destroyed will reveal the Map. The other passage leads to a battle with a Dead Hand, the creature you fought at the Bottom of the Well to gain the Lens of Truth. Against this Dead Hand, you can use the Lens of Truth to see where the floor is different, then place a Bomb there to flush him out. I usually don't bother with this option; just get caught by one of the hands, struggle free, then attack the head of the creature repeatedly.
Once you have both items, go back to the room where you found the passage leading to the Map and Hover Boots. Here, there is a bird sitting on a perch and nearby is a spiked slate with the Emblem of Time on it. Using the Lens of Truth, spot the real skull and have the slate pointing to that skull. This will open the door on the far side of the pit, so don the Hover Boots to reach it; choosing a fake skull yields a bottomless chasm. After you cross the pit, go down the slope to the Beamos statue, then go through the left passage.
Here, avoid the spinning blade and collect all of the Silver Rupees, and make sure you keep using the Lens of Truth to spot danger zones. Your reward is a Key, and after recovering it you should exit this room the way you came in and then run accross to the passage on the opposite side. Here, hack 'n' slash the two Gibdos to recover the Compass. Exit the room and drop a Bomb to clear the last passage you haven't explored at the intersection Beamos guards. Go through the locked door, and beware of Giant Skulltulas as you proceed down this passage. You'll eventually come to some guillutines, which are easily passed by waiting until the blade drops, then running into the flat of the blade; when the guillutine rises up, you'll run past it undamaged.

You'll eventually come to a grassy patch, where you must jump to another platform. Beware, since a Wallmaster will drop here. Jump accross the gap, run along the platform while avoiding the rest of the guillutines and ignore the flaming skull that appears. You'll come to a platform with a Stalfos Knight, so kill him outright or knock him into the pit. Once he's gone, don the Hover Boots and when the elevator platform on chains starts to fall down, run onto it. When the elevator platform reaches its highest point, jump onto the large grassy area with switchblades. Shed the Hover Boots and toss a Bomb onto the Beamos, then gather up the five Silver Rupees and enter the opening door.
Use the Lens of Truth to find a block, then push it along the path for protection against the falling spikes. When two sets of spikes start falling onto the block, stop pushing it and go to the other side and start pulling it. Pull it as far as you can, then use the block as a stepping stone to reach the top of the rear spike set. From here, jump left and activate the switch to reveal a chest, which is reached by grappling it with the Longshot. Get the Key from the chest, then drop down and return to the previous room. Again, use the Hover Boots to reach the elevator platform, and when it reaches the top jump to the narrow platform. Continue along here, using the Lens of Truth to reveal hidden moving platforms and reach the locked door on the other side.
This next room is guarded by a ReDead and invisible spikes. Knock out ReDead and avoid the spikes with the aid of the Lens of Truth. Gather the five Silver Rupees, using the Lens of Truth to spot helpful Longshot targets. Go through the opening door, then climb up the stairs while avoiding the bats and Fire Keese. Toss a Bomb Flower into the flaming skull to reveal a Key, then eliminate all the hostiles to return to the previous room. Now, see that large platform? There's an invisible Longshot target in the roof above, so grapple it and go through the locked door.

Here, you must negotiate a series of passages guarded by powerful fans. Don the Iron Boots to be securely anchored to the ground, and your only problem then is the switchblades. You'll eventually drop down to a fenceless gantry with lots of fans on the side. On the far side of this passage is a room of basically no consequence, but use the Lens of Truth along the gantry to spot a hidden passage. Get into position so that the fans can blow you accross this passage, then don the Hover Boots to reach it. Remember that above the door to the no-consequence room, there is a fake Eye Switch that lobs flame every now and again.
Get rid of the all the hostiles which adorn the next room, then Bomb the bric-a-brac near the entrance. Use the Lens of Truth to find the chest with the Key, then go through the locked door. In this next room, follow the path to a movable block, then push it so that you can reach the ladder. Climb up the ladder and board the boat, then play Zelda's Lullaby on the Triforce symbol to get it moving. As you go, two Stalfos Knights will appear and should be disposed of quickly. When the boat comes close to the end of its run, it'll start to sink so watch your position on the Map so you can know when to stop your Stalfos combat and jump to the stable platform.
Go through the nearby door, using the Lens of Truth to see where this maze's walls are. There are three rooms accessed through here: one has three rotating flaming skulls which, when you throw a Bomb Flower into one of them, reveals a whole heap of Rupees. Another has a single invisible Floormaster who reveals a Key when he's destroyed. The final door opens with wooden spikes trying to sandwitch you: cast Din's Fire (Fire Arrows won't work) to burn the spikes away. Destroy the ReDeads in this room and recover the Boss Key. Once you've swept all of the rooms coming off the invisible maze room, go back through the first door and return to the platform you landed on to escape from the sinking boat.
Look across the long chasm and you'll see some Bomb Flowers. Hit one with an Arrow to set them off and cause a statue to fall and create a bridge. Cross the bridge and go through the locked door. In the final room, use the Lens of Truth to see the stable platforms and use the Hover Boots to reach them. Go through the final door to find yourself on the skin of a drum. And who is playing this drum? Why, it's none other than....

BONGO BONGO: Phantom Shadow Beast
Equip the Lens of Truth and the Bow for this fight. You can also equip the Longshot, but it moves too slow to be effective. If Bongo knocks you off the drum, run straight back for the drum and climb back onto the battlefield because the toxic waste will drain your life like you wouldn't believe. This battle is long and perilous, so it's a great idea to have Biggoron's Sword for this fight.
Bongo's hands are always visible, but his head and torso can only be seen with the Lens of Truth. Bongo bangs on his drum, causing Link to bounce up and down. He'll then bring one hand out to attack, trying to knock Link off the drum. If Bongo doesn't use his hands, he'll use his torso to ram Link. When you hit one of Bongo's hands, he'll release either some Arrows or a Magic Jar.
Lock onto one of Bongo's hands with Z-Targeting, then fire an Arrow to injure them. Bongo won't take damage, but the hand will turn blue and be out of commission for a while. Do the same to the other hand, and when both are injured activate the Lens of Truth. You'll see Bongo getting his torso into position to ram you, so lock onto his eye and hit it with an Arrow. Now rush in and slash away at his eye with the sword; Jump Attacks are a great idea. When Bongo recovers, deactivate the Lens to conserve Magic Power and repeat the attack from the top.
Remember that Bongo's hands aren't vunerable all the time. I find it best to hit the hands when Bongo's playing the drum or when he's winding up an attack, but not when he's performing the attack. Take advantage of the Arrows and Magic Jars Bongo drops when you injure his hands as well. When Bongo has taken enough punishment, he'll dissolve into nothingness and leave a Heart Container behind. You're now welcome to enter the warp and enter the Temple of Light for the Shadow Medallion.

"Anyone who seeks fame need only become familiar with all that I have acheived." - Claudius Galen
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