Go to the right, follow the passage and pick up the Map from the chest. Then, follow the other path to the left, pick up the nut all the way to the left, throw them at the door while being not too close to destroy the vines and open the door. Jump down, get rid of the plant and pick up the stick it drops. Go to the chest inside the tree trunk, and set the vines covering it on fire to pick up the Knight's Crest. Use the purple flowers and the Deku Leaf to get back to the main floor, then to reach the second floor north. Cut the bushes to find a Bomb Flower, then throw it at the door and open it. Now use the Leaf on the sort of leafy pinwheel on the left to bring the hanging platform close to you. Jump on it, turn back to face the door you came in from, and use the Leaf to propel yourself to the other side of the room. Open the door.
Start off by defeating the enemies with the Deku Leaf, and by slicing them with your sword once they're down. Get rid of the north-west Baba, then jump in it and in the next one to reach the second level. Use the Deku Leaf on the leafy pinwheel, jump on the platform and get across the room. Pick up the nut behind the planks, bring it on the platform, then go across towards the door. Pick up the nut again, jump, destroy the vines on the door and open it. Use the Leaf to make the nut roll a little further away, then throw it on the door and go on. Use the Grappling Hook on the right, jump on the moving branches and go north. Pick up the nut, throw it on the western door and open the door. Cross the gap, go ahead and open the next door (use the spin attack to clear out the black creatures).
Keep going on while avoiding the green tentacles, pick up a Bomb Flower on the left and throw it at the planks. Pick up the Compass from the chest, then grab another Bomb Flower and use it to blow up the planks further away. Then, walk around the room to go to these planks and pick up the Small Key from the chest. Jump into the purple flowers and pick up a Joy Pendant from a vase at the top. Backtrack two rooms, then jump left and unlock the door. Cross the room using the pinwheel and the Deku Leaf while on the platform, and open the next door. Use the plant to climb up, go west and climb the other plant. Open the door north.
Hit the butterfly to shatter its wings, then aim at and hit its tail. Pick up the Boomerang from the chest! Throw the Boomerang on the two points above the door and let go to unlock it. Get out and throw the Boomerang to finally get rid of the flying enemies. Use the Grappling Hook on the right, climb the rope, use it on the second bar and jump on the branch. Then, go on the next branch and when you're at the very top, jump towards the chest in which you will find another Joy Pendant. Go back down, use the Boomerang to unlock the door and open it. Get rid of the flying creature, then use the Boomerang to aim at and cut all the vines hanging from the ceiling. Fly straight ahead using the Deku Leaf, pick up a Joy Pendant from the chest and go forward.
Take a look at the great flower hanging from the ceiling, then cut all its appendices using your Boomerang, so it will fall down and break open a hole in the ground allowing you to reach the underground. If you can contact Tingle, fly to the second floor to the west, jump on the two moving branches, then on the ledge and drop a Bomb on the leaf pile to unlock a warping point. Jump all the way down to the bottom.
Upon landing on the flower, open the door to the left. Use the Boomerang to get rid of the enemies, then jump on the platforms, go north to the other side and open the door. Jump on the brown flower, then cut the vines to fall along with them. Go left, throw a Bomb Flower on the planks and open the door to the north. Clear out the enemies, then go to the back of the room. Get rid of the Baba north-west of the room, jump in and use the flowers and Deku Leaf to get on higher grounds. Use the Leaf again to go across on the platform, grab a Bomb Flower, go back on the platform and throw the Bomb into the big open trunk. Jump down into that trunk, or get inside by the north-west path, and pick up the Treasure Chart from the chest. Leave this room, climb the ladder on the left, jump on the flower and slash its vines again if you need to. Use the Deku Leaf to move the flower around the water and get rid of the enemies using the shield. Go forward and open the door to the right. Follow the path to reach the top of the trunk, then aim at the five glowing buttons with the Boomerang. Pick up the Big Key from the chest, fight the two guardians and get back on the trunk. Use the Grappling Hook to reach a platform to the east and open the door.
Jump down, go forward on the platforms and open the door to the east. Use the Leaf on the leafy pinwheel to create a wind current, jump into the flower, then use the Leaf to fly in the current until reaching an upper level (second floor). Then, use the Boomerang to destroy the vines and open the door east. Get rid of the enemies to unlock the doors and pick up a Joy Pendant from the chest. Follow the way up to the next room. Cut the nuts to find a small fairy and put her in your bottle, then pick up a stick from the vase and burn down the planks on the big vase to the left. Finally, open the door leading to the boss.
Get close to the flower in the middle of the room so it closes and hangs itself from the ceiling. Using the Boomerang, do your best to quickly aim at five of its appendices to cut them. Move around to avoid the tentacle attacks, and repeat these steps until the plant falls down. Now, run to its centre and hit it with your sword as much as possible before it spits you out and climbs back to the ceiling. Keep on cutting down the appendices and do this twice to three more times to defeat the boss once and for all. Pick up the Heart Container and get into the light beam.
To thank you, the Deku Tree will give you with the Farore's Pearl he promised you. After the celebration, talk to Makar who stayed close to the Deku Tree. Pay a visit to Hollo's Potion Shop if you want to, then leave this place and go back to the King of Red Lions. Take a look at the mailbox swinging around to pick up a Piece of Heart.
If you only found one Treasure Chart in the dungeon, you can go back there. Go back to the second room, climb north to the second floor, then to the third to the south-west using the plants, and cut the vines with your Boomerang to open the chest containing the Treasure Chart.