Your first objective when you enter the Great Deku Tree is to make it to the top of the this room, which is the main room. First, scrounge the bottom floor for items and what not. Then proceed up the ladder. On the way up you will reach a treasure chest containing the Dungeon Map. Continue up the ramp until you reach the door at the end and enter it.
All you have to do to defeat the Deku Scrub is target him and hold R. He will shoot a Deku Nut at you, which will reflect off your shield and hit him. Then proceed through the next door. Jump across the platform, and be quick, as the platform will fall. Open the chest and you will receive the Fairy Slingshot. Look back to where the platform fell and you will see a ladder on the wall above, which Navi should fly to. Use your Slingshot to shoot it down. Then exit the room.
Head back to where you picked up the map and use your slingshot to shoot the spiders off the wall. Then climb the wall up to the next platform. Go into the only door here at the top floor.
You’ll find a switch in this room which will make all the platforms rise. First however, head to the crevasse in the south wall and a Skulltula will fall. Defeat it and hit the switch. Go into that crevasse to find a Gold SkullTula. Step on the switch again and go all the way to the other side of the room and open the chest. You’ll obtain the Compass. Now go back to the torch, take one of your Deku Sticks and light it on fire, then light the other torch in the room. Note: save your stick from burning away by pressing B to pull out your sword. Link will put the stick back.
Once you exit you’ll be back in the big, huge, multi-floored room. At the bottom is white webbing, and if you jump from the top floor you can break right through it, so do that now.
In this room you’ll find a Gold Skulltula; you’ll also find a switch on the higher platform (not the highest). Step on it and one of the torches will light up. There is a chest right beside that torch. Light a stick on fire, and jump down to the lower platform without losing the fire, and light that wall of webs on fire. Then head through the door.
A Deku Scrub, you know what to do. Remember the order this Deku Scrub gives you. For me its 2 3 1, but I don’t know if it’s the same for all. The door in this room has an eye above it. Shoot that eye with your Slingshot and the door will open.
This room is very simple. Find the switch underwater, dive in and press it. Just use your shadow to judge where you are. Then go back to the ledge and jump on the floating platform and ride it under the spike poll. Once across, kill the Skulltula and push or pull the block over. Then climb up into the next door.
In this room light both the torches and the door will open.
Take out the enemies in this room, and then use the Deku Sticks to light the web walls on fire. One of them has a small tunnel that Link can use to get into the room you started in on the bottom floor. Now push the block you see off the ledge. After that, light up a Deku Stick, jump across the platform onto the block and light the webbing on the ground on fire. If you can’t seem to get him to touch the web with the stick, just roll (By pressing A while moving). Jump down the hole.
In this room you have to kill the Deku Scrubs in the order the other Scrud gave you. Once you kill them in that order the last one will reveal how to defeat the Queen to you and the door will open.
Now you’re in the boss room. Wander around this room all you want, take the items, and explore. When your ready to continue look skyward.
Queen Gohma
Queen Gohma will try to attack you, and when she does her eye will turn red. Once it does, hit it with your Slingshot. Remember to use Z or L targeting. Then, when she’s knocked out hit her in the eye with your sword. Hit her enough times and she will die. Congratulations, you win!
Once you get out it's time to make your way to Hyrule Castle.
