The instruction manual is 48 pages of in-depth explanations, devoting 6 pages to backstory alone.
The manual describes how Ganon got his hands on the Triforce, corrupted the Golden Land, and became a beast.
After vanquishing his own followers, the leader stood triumphant before the Triforce and grasped it with his blood-stained hands. He heard a whispered voice: "If thou hast a strong desire or dream, wish for it..." And in reply, the roaring laughter of the brigand leader echoed across time and space and even reached the far-off land of Hyrule.
All is lost, the villain has flown off, there's no possible way to follow him... fade to black... ...cue ocarina, summoning the stone duck across the dimensional divide...
Agahnim is probably one of the most competent Zelda villains; he kills the King and apparently vaporizes the maidens, including Zelda—the latter right before Link's eyes. When he's defeated the first time, he transports Link to the Dark World.
The fight where you have lightning and magic spells thrown at you by Agahnim. It's so cool how you can deflect them with your butterfly net.
This is the first game in the series where Ganon has the entire Triforce. Link still wins.
All three medallions. But the Bombos one especially. Greatest. Gamebreaker. Ever. What do the medallions do, you may ask? Let's see:
Ether: Link waves his sword and a bolt of blue lightning strikes it, the screen turns dark, and ice crystals revolve around him, freezing most ground enemies and killing flying ones.
Quake: Link jumps into the air and stabs the ground with his sword. Purple lightning courses across the room, and ground-bound enemies are killed or turned into slime.
Last but not least, Bombos: Link swings his sword, and an arc of flame spirals out around him, before creating bursts of fireworks around the screen, stopping enemies in their tracks and setting them on fire before destroying them.
The Golden Bee gets one any time you let it out in a room full of Wizzrobes, after which it wipes them out in a matter of seconds.
Same thing if you let it out against Mothula. Forever showing that shiny metal bees are more awesome then giant evil butterflies!