Because of the auras of monsters in this temple, you won't be able to dowse to track Zelda while in the temple. Save at the bird statue nearby. You can use the temple's bird statues to go outside if you wish.
Make the Water Rise
Kill the Keese, then cut through the spiderweb, shaking the Nunchuk and Wiimote if you get stuck. Cut through the trees just beyond that. After passing more spiderwebs and keese, you reach some trees blocking some vines on the wall. There is a Deku Baba at the top, so shoot it with your slingshot, then dash up the wall to get there before the Deku Baba recovers. Kill the Deku Baba, then hit the switch to open the locked door.
Beyond, there is an eye on the wall. If you take out your slingshot, the eye goes away. A sign at the lower level says to ask your servant for advice. Lock onto the eye then press down for Fi's advice. She says that the eye looks at pointed objects. So take out your sword and slowly move the tip in a circle over and over until the eye spins out of control and falls to the ground, unlocking the door.
Beyond, there are Deku Babas on the ceiling. Try to avoid the burrs, kill the Deku Babas, then continue on.
Save at the Bird Statue. There are Walltulas on the vines behind you. Use the slingshot to kill them, then climb up the vines to reach some wooden barriers. Use the sword to cut the barriers. This gives you a shortcut.
Go back the way you came. There is a Green Bokoblin up ahead. It's pretty much the same as a Red Bokoblin. It just prefers underground places.
Up ahead, there are three doors. The middle one requires a key, but you can open the other two. To open the door on the left, hit the switch under the bridge that leads to it. The area on the lower level has a bunch of hidden rupees, so go around and get those after you hit the switch for the door. To open the door on the right, hit the switch that you can see right above it.
Make the Water Rise More
If you go through the door on the left, you find a bridge blocked by Skulltulas. Use the slingshot to knock down the vines to the right of the bridge, then swing across to the other side of the room. Kill the nearest Skulltula with forward thrusts, but don't get too close or you will get hit when the skulltula shakes back and forth. Cut through the webs, then go to the middle of the bridge and turn to the side to see a pink switch in the wall. Hit it with the slingshot to make the water level rise. Then go through the door up the stairs.
Get the Map
You will be back in the central room from before, but you are up on a ledge where you can reach a treasure chest. It contains the map. It will show you where treasure chests and other items are, as well as the location of Zelda's Aura.
Now drop down to the lower level and go through the door on the right that you opened by hitting the switch above the door. You can optionally kill the Skulltula blocking the sign, which mentions the switch hidden under a bridge in the central room. Hit the Skulltula with the sword to make it spin, but move around to prevent the Skulltula from swinging into you. Once you can see its stomach, use forward thrusts to kill it. Then you can read the sign.
Don't climb down the vines. There are Walltulas on them. Just jump down, then use the slingshot or your sword to kill the Walltulas. Walk around this lower area to find a small hole in the wall that you can crawl through. Hit the switch in this small room to make the water level rise. Swim over to the vines and climb up, then go through the small hole here to get back to where you were.
Get a Key
Return to the central room. With the water level up, you can walk on a log to reach the vines on the wall. Climb up to reach the room that you were just in. Hit the Skulltula to make it spin, then use thrusts to kill it. Fi will tell you about the eyes. Stand in the middle so that both eyes are looking at you, then spin the sword in a circle repeatedly to make the eyes break. Get the key from the chest beyond, then return to the central room. Climb up the vines and use the key on the door in the back.
Get the Beetle
In this large room, use the slingshot on the pink switch above the door in the central pillar. Go through the door that unlocks. You will find a Stalfos. Get your shield out. Strike the Stalfos with your sword until it does a sword attack. Use a Shield Bash as it does the sword attack and its arms will pop off, allowing you to hit it repeatedly with your sword until it is defeated.
When it's gone, a chest appears. It contains the Beetle. You can launch it by pressing A. You can use the Wiimote to control it as it flies through the air. If it collects items like Rupees during its flight, you will receive those items when it returns. Make the Beetle fly through the spiderwebs in the wall, then make it hit the pink switch outside that you used to unlock this room. The door will unlock again, allowing you to leave. Go back out to the central room.
Get a Second Key
Use the Beetle to cut down the spider webs that hold up some boxes. One of the boxes contains a fairy. You can empty one of your bottles and use it to catch the fairy (no need to use the bug net.)
Go to the locked door on the west side of the room near the bird statue. Fly the Beetle into the passageway above this locked door. The Deku Babas will not attack the Beetle, so just make the Beetle avoid them, then bump into the pink switch. The door will unlock. Go through.
Drop down to the lower area and go through the door beyond. A Skulltula will drop from the ceiling. Swing the sword upward to flip it over, then swing the Nunchuck and Wiimote down for a fatal blow. Climb up the vines and use the Beetle to cut the spiderweb that is holding the boxes. Push the unbroken box to the lower level and push it in the middle of the three eyes. Climb up onto it. If you positioned the box correctly, all three eyes will open. Spin the sword repeatedly in a slow circle to make the eyes break and fall. Get the small key from the chest.
Get the Golden Carving
Go back to the previous room. Fly the Beetle past the Skulltula's web and make it hit the pink switch to raise the water level. Then swim and walk over there, kill the Skulltula, chop down the trees and climb through the small hole to reach the door.
Back in the big central room, go to the opposite side of the room. Use the beetle to cut down the Deku Babas, then climb across the rope and unlock the door to reach the next room.
There is a Staldra in here. You have to hit all three heads at once, so wait for the heads to be in a straight line, then swing the sword in the direction of that line. Once you defeat it, the door will unlock.
In this room, use the beetle on the pink switch to unlock a shortcut to the large central room. Use the beetle to knock down the vines on the left side. The Green Bokoblin is scared of the beetle, so use the Beetle to make the Bokoblin fall into the pit. Walk across the rope to the other side of the room, then turn right to reach some vines. Climb up and you will soon reach the swinging vines. Use the swinging vines to reach the Golden Carving, which unlocks the door in the back where Zelda's Aura shows up on the map. Climb up the vines and go toward the door in the back, but before you go through, turn left and open the small chest to get a red rupee.
Unlock the Boss Door
To unlock the door, you have to press A to hold the golden carving, then rotate the Wiimote to make the carving match the shape of the opening. Look for the outline of the Wiimote in front of the carving to help you figure out how to rotate it. Rotate the Wii Remote as if you are holding the golden carving. Once it's correct, the carving will glow and you can press A to insert it. Then the door will unlock and you will go through.
Now you meet Ghirahim. He'll say that a servant of the Goddess took Zelda from him. Then you have to fight him.
At the start of the battle, he won't use his sword. Point your sword and wait for him to keep his hand still, then slash from a direction that is far from his hand. For example, if he holds his hand on the left side, swing from the right.
After you do enough damage, he will take out his sword. If he is far away from you, he will send some floating energy things at you. They will be in a line going in a certain direction. When they get close, slash your sword so that you hit all of the floating things (similar to the strategy for killing the Staldra), and they will fly back and hit him. If you don't swing correctly, you will take some damage.
If Ghirahim appears close to you, quickly look at where he is holding his sword and slash in a direction that avoids the sword. For example, if he is holding his sword vertically on his right side, swing the sword horizontally from the left. Otherwise, if you hit the sword, he will hit you. Once you hit him, keep hitting him until he goes away. If he is dashing toward you, just swing the sword to hit him before he crashes into you.
After you do enough damage, he will give up and disappear. Get the heart container and open the door. You will reach Skyview Spring. Go to the far end of the area. Use a Skyward Strike on the floating crest in the back. Fi will translate a message for you that says that Zelda has purified herself at this spring and will continue to the Earth Spring in Eldin. You will receive the Ruby Tablet, which Fi says to take to the altar back in Skyloft. When you go outside, a Kikwi will thank you for your help. Use the bird statue to return to Skyloft.