On the way to the Forest Temple, you will encounter some skulltulas. These are easy enough for your homing cannonballs to defeat, or you can blow your train whistle when you get close, and scare the things away.
Once in the Forest Temple area, you will see another of those stone rockets with lights floating out. Approach it and play your flute nearby to learn the Song of Healing. This song can only be used in a dungeon, and will summon a fairy to heal you up to full health, but you can only use that song once per dungeon.
Now, ahead of you is a locked door. Go to the right and you find some nuts growing from the ground. Pick one up and walk up and to the right. The path up here takes you to a switch that you can activate with the nut. Cross the bridge that appears, and soon you will be face-to-face with some enemies. Defeat them to make a treasure chest appear. The door will then unlock. Go down the stairs.
There is purple fog in here. It's poisonous, so don't let Link walk into it. Go to the northeast, where you must fight some more enemies. They leave behind some poisonous gas, so avoid walking toward that. Open the chest in here and you receive a special item called the Whirlwind. When equipped, you can change the direction where Link points the Whirlwind using your stylus, and you can make wind blow out of it by blowing into the DS Microphone. The Whirlwind can blow away poisonous fog and can be used for many other purposes.
Back in the southeast part of the room, blow the fog away to get a treasure chest. Then in the area where you received the Whirlwind, use the Whirlwind to blow the spinning switch, making the door open.
Go through the newly opened path and there's a statue there that you can wake up with the Song of Awakening. This statue, and others like it in other dungeons and on other floors of this dungeon, will let you know if there are any treasure chests around.
Use the Whirlwind to clear the fog so you can go down the stairs.
You'll see a key here that can't be reached. Just use the Whirlwind to blow the key to a place that Link can walk to. Get the key, then go right and press the switch to open the door. After you defeat the fog spiders in this area, go north and blow away the fog to find the stamp station. There is also a switch here, which will make a chest appear.
Go back across the bridge that you crossed a moment ago to get the chest, then go to the center area of the floor to unlock the locked door here with your key. In this new room, you will encounter some fog Bubbles. You will need to blow away their fog with the Whirlwind and then strike with your sword while they are stunned.
Continue to the stairs. Continue going north to find more stairs, up to the third floor. You will see a crystal switch across a gap in the floor, as well as a nut on your side. You should stand in front of the nut so that there is a straight line from you to the nut to the crystal orb. Then you should use the Whirlwind to blow the nut into the crystal switch, activating it.
Get the key from the chest that appears. Go downstairs and go toward the east to find another locked door. Use your newly-found key in it.
You will reach an area where Mothula will attack you. It flies around, and occasionally it will turn red, after which it will shoot a fog bubble at you. When Mothula does this, you should use the Whirlwind to shoot the bubble back at it. But don't use the Whirlwind too early, because if you use the Whirlwind before there is a bubble coming at you, then Mothula will blow the gust of wind back at you, stunning you before swooping in to attack you. When you successfully hit Mothula with a bubble, it will be stunned, and you can run over and slash with your sword. The grass in this room gives you hearts if you need them.
With Mothula out of the way, go upstairs. Go west and south, and you will encounter a worm that follows you slowly. This type of worm will roll into a ball if you hit it, and shortly afterward will explode. You can use this worm to blow up the blocks in this room. Lure the worm near to the blocks, then hit it with your sword. If you weren't able to make it go close to the blocks, you can use the Whirlwind to blow it over to the blocks. Once it explodes, go through.
Blow the fog out of the way, and step on the switch to make a treasure chest appear. After getting it, hit the crystal switch to open the door.
Go through the door that you opened, and use the blue worms to break the blocks out of the way and activate the crystal switch (you will need to use two worms). This will open a door that gives you access to the big key! Take a look at the map behind the big key. The red line tells you where the safe path is. Copy that line onto your map. If you stray from it, monsters will appear to take the key and put it back in the room where you first got it. Follow the line and put the big key into the lock at the end.
Head upstairs and you will have to fight Stagnox.