Part 2: Southern Swamp
Head back to Clock Town after talking with the Mask Salesman. Tatl will initiate a brief dialog. Afterwards - head forward and through the gate. The guard will stop you momentarily, but allow you passage to Termina Field. Continue south for a cutscene with Tatl and continue once more afterwards.
You will enter a new area with no access to a map. So continue a short ways to find Tingle floating around. Use the Deku Mask and shoot Tingle down with a bubble. Purchase the map of Woodfall for 20 rupees. If you do not have 20 rupees - cut some of the grass nearby to get rupees. Continue south to find the Southern Swamp.
Continue south and a cutscene will happen with Kaepora Gaebora - an owl - and you will learn the Song of Soaring, which allows Link to warp to any activated Owl Statue. Continue southeast after activating the Owl Statue to find some lily pads. Climb onto the first one and water hop across to the next one.
Continue going across to each lily pad until you reach land. Head east down the path towards the Magic Hag's Potion Shop. Continue to the north and enter the Woods of Mystery. Talk to the monkey and follow quickly follow him. If you lose sight of the monkey - listen for monkey noise and go that direction.
You will eventually come across a wounded witch by the name of Koume. Speak with her as normal Link - that is without any masks on that change your appearance - to learn about her situation. Now exit the woods and enter the Magic Hag's Potion Shop. Talk to Kotake to get the Bottle of Red Potion.
Travel back to Koume and give her the red potion for a short dialog. Afterwards - you end up with an Empty Bottle and a free boat ride offer. Use the Song of Soaring to warp back to the entrance to the Southern Swamp. Cut some grass here for a Deku Stick, but this is not required. Head south and enter the Swamp Tourist Center.
Talk with Koume to get the Pictograph Box as well as a free cruise. Ride the boat to the other side of the swamp. Answer yes when you reach the next dock. A cutscene will ensue with a monkey. Follow the monkey inside of Deku Palace. Equip the Deku Mask and talk with the Deku Guards across the bridge.
Continue inside the Deku Palace and go to the Royal Chamber. A cutscene will happen with a trapped monkey. Travel up to the cage and speak with the monkey. Take off the Deku Mask to be thrown out. A dialog will happen with another monkey. Go to the Inner Palace Garden and continue down the path.
Be sure to dodge all of the guards and fall into the hole at the end. Talk with the Bean Seller to receive Magic Beans. Travel a short distance from the Bean Seller to find a spot of water. Use the Empty Bottle to get some Spring Water. Now use the portal across the spring to reach the Outer Palace Garden.
Plant the Magic Bean in the soft soil nearby as normal Link by standing on the soil and using it. Use the Spring Water on the Magic Bean to make it grow - or this can be achieved by rain as well. Use the plant to reach the upper area of the Deku Palace. Equip the Deku Mast and continue into the palace.
Drop down and use the Deku Flower to reach the next platform with another Deku Flower on it. Ride the platform across and shoot a bubble at the Deku Scrub. Now use the Deku Flower to fly over to the next platform. Continue this pattern until you reach the next passage. Continue through the short hallway.
Now shoot a bubble at the Deku Scrub and use the Deku Flower to fly over. Use the next Deku Flower to reach the next platform. Continue killing the Deku Scrubs and using the Deku Flowers until you reach the upper leave of the Deku Palace. Enter it to find yourself inside the Royal Chamber once more.
Drop down and talk with the money as normal Link. Now attempt to cut the rope holding him hostage. Equip the Deku Mask and pull out the Deku Pipes. Answer “Yes” to his question about the situation. The monkey will now teach Link the Sonata of Awakening. Link will now be kicked out of the Deku Palace.
Water hop across to the lily pad to the east and continue to the small ledge with the Deku Flower and sign. Use the Deku Flower to fly up to the opening and enter it to be back in the Southern Swamp. Continue to each platform by using the Deku Flowers, being sure to dodge the enemies or kill them.
Getting to Woodfall Temple
Save at the Feather Statue if you wish and continue inside the door to find Woodfall. Travel around the west side of the map and kill the enemies along the way. Kill the Mad Scrub to find a Deku Flower. Use the Deku Flower to travel across to the cliff with the cave. Kill the Mad Scrub across the way.
Now use the Deku Flower to reach the platform. Continue across it and kill the next Mad Scrub. Use the Deku Flower to reach the platform, which has the Deku Scrub Mark on the floor. Activate the Owl Statue and now play the Sonata of Awakening. This will raise up the Woodfall Temple. Use the Deku Flower to reach it.