Inside the Deku Tree
Note: Try to get the maximum of seeds (30) for the final boss. You will also need several Deku Sticks during the course of this dungeon.
Go ahead and climb the ladder on the left. Walk and jump towards the chest and open it to find the dungeon Map. Keep going until you reach a door on the left. Get in and attack the Deku Scrub: stand in front of it and raise your shield when it shoots at you. When it is hit, run to it so it will give you a clue.
Open the next door, jump to the other side of the room and open the chest containing the Fairy Slingshot. Climb the vines to the left, open another chest containing a small heart, then go down and stand in front of the ladder hanging from the ceiling. Shoot at the ladder with the Slingshot, then get out using the ladder and come back to the chest which contained the Map. Get rid of at least one of the Skullwalltulas above the chest with the Slingshot and climb while avoiding the other one a little bit higher! When you've almost reached the top, move to the right and let go at the end.
Walk around the web while avoiding the big Skulltula until you reach a door. Open it, stand on the switch to the right, then go to the back of the room by jumping on the three platforms and open the chest to find the Compass. Go back to the other side, step on the switch, jump on the platforms, but this time go left. Open the chest if you need a heart and get rid of the Gold Skulltula (the spider) to get a Token. Go back to the switch, light a Deku stick with the torch and light the other torch quickly. Get out and fight with the big Skulltula on the main web: wait for it to show you its back and use your sword. After beating it, you only have to jump to make it through the web and you will reach the first underground level.
Climb on the platform with a switch, step on it, then open the chest. Next (you have to be fast), light a Deku stick, turn around, jump into the shallow water, then jump on the platform in front of you and burn the spider web to discover a door. Get in, defeat the Deku Scrub and take note of its clue (2 3 1). Shoot at the eye above the door with the Slingshot, then open it. Here, dive into the water and go press the switch on the left. Quickly come back on the bank and jump on the moving platform. Jump to the other side, get rid of the Skulltula then push the block as far as you can. Climb on it, climb on the top of the wall and open the door. Light a Deku stick and light the two other torches, and then open the unlocked door.
Get in the new room, first get rid of the Skulltula, then burn the two webs. Get in the narrow path to the east. You arrive in the first room of the first basement. Notice the web on the ground, and push the block on your left, climb on it and go to the other platform (already visited). Better be swift: light a Deku stick, go back to the previous platform and burn the web by "attacking" it with the stick. Jump into the hole, swim towards the three enemies and attack them like the previous Deku Scrub, but in the specific order: middle, right, left (2 3 1). When the last enemy is hopping around, run to it so it gives you another clue to defeat the boss.
Queen Gohma
To defeat it, you have to shoot at its eye with the Slingshot when it turns red, then while it's paralyzed, use your sword relentlessly on its green eye, doing so three times! Each time it climbs back to the ceiling, it drops three larvae that you have to slash with your sword. However, if you hit the Queen with the Slingshot as soon as it has climbed back on the ceiling, you will avoid those larvae. If you need more seeds or small hearts, you can cut the bushes near the walls. Once defeated, pick up the Heart Container and enter the blue light.
After thanking you, the Great Deku Tree will tell you about a vile horseman from the desert and about the creation of the world, the Goddesses and the Triforce. He will warn you against this desert man, then asks you to go to Hyrule Castle. Finally, the forest sage gives you the Kokiri's Emerald.
Back in the forest, talk to Mido, then go through the forest to the west until you reach a large opening in the stone. Go through this passage and meet Saria, who will offer you the Fairy Ocarina before saying goodbye.