This part will take you up to the final boss fight
As Link enters the chamber, he sees a female figure sleeping on a bed behind a curtain. It is Zelda, and sitting over her is the figure of Ganondorf. He tells Link that he can see her dreams -- dreams of oceans as far as the eye can see. Yet he says that these oceans are barren of life, and they are too wide to swim across. He even scoffs at the idea that the people of Hyrule fled to the mountains so that they might one day resurrect the kingdom, telling Link, "Your gods destroyed you!" The curtain parts and Zelda disappears as Ganondorf transforms into a hideous giant puppet, the first of three forms Link will have to fight of what is called Puppet Ganon.
His first form
Puppet Ganon's first form is that of a giant puppet that's held up by strings. It uses its arms and swings its tail to attack. Use the Boomerang to snip at all the strings so that its glowing blue tail hits the ground and is immobile, then get out your Light Arrow and strike it. The strings will then regenerate. Repeat this tactic until he is defeated. Link will rejoice at his defeat, but it is only temporary, as Puppet Ganon now changes into another form.
His second form
Puppet Ganon's second form is that of a giant spider that will spin around the ceiling of the room and then drop down on you when you least expect it. Using a technique that was later employed in Twilight Princess with the Snowpeak Ruins boss Blizzeta (but that's a whole other story), the water on the ground will reflect where the Spider form will most likely drop down, so watch the reflection and prepare to stand out of the way when it falls so you can strike the glowing tail with the Light Arrow. Not making things any easier are the presence of Keese that will swarm around you. Strike them down quickly to get them out of your way. When the Spider form is defeated, Puppet Ganon will transform one more time.
His third form
Puppet Ganon's final form is that is a giant Moldorm that quickly scurries around the arena in an attempt to ram Link. Again his weak spot is the glowing blue tail that you must strike with the Light Arrow. However, because the Moldorm form moves around so erratically, it's difficult to get a good shot at the tail. If you've got All-Purpose Bait, stand around the center of the arena and then throw the bait into the water. The Moldorm form will then be attracted to it and start moving around in circles in that spot, giving you a good chance to strike the tail. During this fight, you'll also be bothered by the annoying sticker bugs that will latch onto you. Do a spin attack to get them off you as quickly as possible. When the Moldorm form is defeated, Ganondorf will congratulate you before disappearing again with Zelda.
Ascending the Tower
Climb up the rope to the rafters above you, then use the Grappling Hook to latch onto the pole the next level above you so you can climb up to there. Go to the center of that rafter and smash the skulls to replenish your hearts and magic, then Grapple Hook your way onto a pole another level above you to climb up to. Go to the center again and bomb the teleportation pot so you can have access back to the staircase where you can save your progress. Then go over to where you see a giant window and Hookshot your way over there so you can step into the blue beyond and face Ganondorf for the last time.
Final Boss: Ganondorf
As Link reaches the top of the tower, Ganondorf tells his tale of woe, how his people have suffered winds that brought nothing but death and that he envied the breezes of Hyrule. He says it seems fitting that he should gather together the three with the Triforce crests so that he could have his wish granted by the Goddesses. Already he has the Triforce of Wisdom in his grasp, and all that remains is the Triforce of Courage. Link gets ready to defend himself, but Ganondorf quickly fells Link, knocking the Master Sword out of his hand. He promises the boy he will not harm him, but merely will gain what he has. As Ganondorf raises up Link by his hand and concentrates, the three parts of the Triforce come out of their hands and form together into the full Triforce. Ganondorf laughs as he approaches the Triforce and drops Link, realizing the power to grant his wish is now in his grasp. He calls out to the Goddesses, demanding them to let the rays of the sun burn forth over Hyrule so that it could be his forever. But before he can touch the Triforce, the King of Hyrule already has touched it and made his wish known to the Goddesses: let Hyrule be washed away forever and let there be a future for the children. Soon water pours down on top of them. Ganondorf laughs maniacally, believing the king's wish to be foolishness. Soon Zelda awakens and hands the Master Sword back to Link, telling him it's time for them to return to the world above. With swords drawn, Ganondorf decides to show the king what kind of future the children will have.
Ganondorf is a pretty tough fighter who can do two hearts of damage to you, so make sure you are well equipped with fairies, Elixir Soup, and as many Heart Containers in your health meter as possible. At the start of the battle, Princess Zelda will use the bow to shoot Light Arrows at Ganondorf. The object at this point is to have Zelda shoot at him when his back is turned, and then have Link slash at him when he's stunned. Be careful not to get hit by the Light Arrows, because they can cause one heart damage to Link. After some hits, Ganondorf will slap Zelda down, which means we're going to have to fight him head-on. Wait for the moment to do a parry attack to stun him, and then give him a few good sword slashes. After some successful parries, Zelda will wake up, but now Ganondorf will be impossible to hit, either with our sword or with Zelda's Light Arrows. Go over to Zelda, and she will tell you to get your shield ready. Here we need to have the shield aimed at both Zelda and Ganondorf so that we can reflect a Light Arrow straight at Ganondorf to stun him. Once he's stunned, rush in to do a parry attack to make Link leap high above Ganondorf's head and drive the Master Sword right into his forehead. Ganondorf will then grunt with a pained sneer as he falls to his knees, muttering, "The wind...it is blowing...", before his whole body turns to stone.
Success!! You've just beaten the final boss of the game.
After Ganondorf turns to stone, the King of Hyrule tells Link and Zelda he has lived facing the regrets of things he wished he could have done differently. He tells them that there may be nothing left for them, but despite the hardships he wants them to live for the future. Princess Zelda suggests that the king could go with them to find a new land that they could call Hyrule. The king smiles fondly at the thought, telling Zelda that that land "will not be Hyrule...it will be your land!" Then the entire ocean floods down on Hyrule, and Link and Zelda float up to the surface in protective bubbles. Link tries to fight the rising bubble in vain, seeking to touch the hand of the King of Hyrule one last time. The king raises his hand as if to say farewell to the children before he resigns to the fate he has chosen, saying to himself, "I have scattered the seeds of the future".
Back on the surface, Link and Zelda (who is now Tetra again) are awakened to the appearance of Prince Komali fluttering overhead, overjoyed that he has found them. Behind the prince they see Tetra's pirate ship coming for them, and on board with the crew is not only Link's sister Aryll but also Medli and Makar, their jobs as sages having ended because of Link's victory over Ganondorf. Link and Tetra smile and wave at them as they wait to be brought on board.
After the credits have rolled, Link and Tetra appear at Outset Island, with Tetra on board her ship and Link on board the King of Red Lions which is now a lifeless sailboat, waiting for the wind to fill their sails. Soon it does, and the two heroes set sail for their next adventure: to find new land for the people of Hyrule. The residents of Outset Island, including Link's grandmother and Aryll, watch and wave goodbye as Link and Tetra sail off into the horizon.
And so the story ends.