Do not buy anything from Beedle's Shop and try to leave. Beedle will open a trap door and you will fall to the ground below.
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Just like Ganondorf in Twilight Princess, you can distract the final boss by taking out either your bug net or larger bug net(if you have it) and wave it around. He will follow the net.
Climb around to the roof over Zelda's room using the ledge by the upper entrance to the Knight Academy. Use the Clawshots on the target on the top of the chimney's reverse side to enter the academy. Note: If done at night, Gaepora will be taking a bath below where you land. Crawl through the passage to enter Zelda's room. Once there you can look at Zelda's Diary by sitting in her chair; get a Gratitude Crystal (at night); get a Heart Piece from the cabinet; and look at the Tingle doll.
When you play your harp around a group of butterflies in specific areas of the game, a Goddess Wall sometimes appears nearby. Hold your sword up to the light, then draw various symbols on the wall in order to obtain the related item. For a group of recovery hearts, draw a heart. For a bunch of rupees, draw a rupee. Drawing an arrow grants you arrows. Painting a circle gives you bombs. And if you can manage to draw the Triforce, you'll get some fairies.