This part will take you through your second visit to Forsaken Fortress.
As you get close enough to the Fortress, lower your sail and cruise your way around the periphery of the place so you can find the gate. However, be careful as you cruise, because you can be fired on by the Fortress' cannons, and also there's a shark in the waters that will bump you out of the boat, costing you time. When you get close enough to the gate, use the boat's cannon to blast it away and then sail on through.
After you get out of the boat, proceed up the two staircases again to the terrace. The next set of stairs after that will be blocked by spiked pegs that we can't get rid of yet. Instead, head for the center of the terrace. You'll see the shadowy figure of a knight appear and then disappear. This is Phantom Ganon, whom we'll be fighting. When he appears, he will charge up an energy bolt to strike down Link with. Strike it with the sword to send it back to the phantom. He will then bounce it back toward you, making it go faster. Here you'll be playing tennis with the energy bolt, with you and Phantom Ganon swatting it back and forth until it strikes either. With each rebound, the energy bolt will travel faster, so time your swing to hit the bolt before it hits you. When it does strike the phantom, he will fall to the ground, allowing you to get some hits on him before he vanishes. He will reappear and play the same tennis game with you. Continue until you succeed in defeating him for good. He will laugh as he vanishes for the final time, as if what you went through was just practice. A treasure chest will also appear, and it contains our next useful item, the Skull Hammer. Link can now use it to smack the spiked pegs out of his way.
Getting to the prison
We'll be following the same path we took the last time we were here, which means we will also have to take out the searchlights so we don't become a target for the cannons. However, there are a few changes. First off, the rooms that once contained lamp ropes to swing across platforms on no longer have them, so we'll need to use our Deku Leaf to float our way across. Secondly, there are pegs that appear which will block our path, so we need to smack them down with the Hammer. Thirdly, in addition to the Bokoblins and the Moblins, we now have gangs of little torturous pests called Miniblins that will dog our steps. Try to get rid of them as quickly as possible. Fortunately, we have the Master Sword on hand to deal with the creeps that we come across, so there's no more stealth involved.
Forsaken Fortress Boss: Helmaroc King
As we enter the prison the second time, Link will try to open the door to let Aryll go free, but he will be interrupted by Tetra, who shows up with two of her pirate buddies. She will tell Link how much trouble it took her to get the big bird off his back so he can get in here to rescue his sister. Tetra has her pirate buddies take the other girls on board so they can deliver them to their grateful parents for a ransom. Soon Gonzo tells Tetra that the bird will be coming back soon. Tetra now has Gonzo take Aryll on board as well where she would be safe. As Link and Aryll wave goodbye to each other, Tetra slips a wink to him before she departs, telling him that she will return for him. Then the big bird swoops down into the tower to take on Link again.
In the first part of our battle with the big bird known now as the Helmaroc King, we need to escape the tower which is now filling up with water. Equip yourself with the Grappling Hook and the Hammer, then proceed up the winding stairs toward the top of the tower. As you proceed upward, the bird will attack and knock out part of the stairs. Keep moving so that the bird knocks out the stairs behind you. If you fall into the water, you can still use the rising water level as well as the Grappling Hook to get yourself up to the top. Also, there will be Bokoblins that will pop out of jars to block your way. Do your best to simply run past them and ignore them. When you reach the top of the stairs, get out your Hammer and hit the Helmaroc King in the head with it. It will fall into the tower, giving you time to climb up onto the top of the tower before it re-emerges.
Now starts the second half of the battle: after it flies around for a bit and lands on the tower, it will either hover over you and beat its wings very rapidly to force you toward the spikes ringed around the top of the tower, or it will attempt to peck at you with its beak and get it stuck in the floor. When it hovers and flutters, try to move towards the bird as much as possible so that you don't get knocked into the spikes. When it gets its beak stuck into the ground, smack it with the hammer. On occasion when it flies around afterward, the bird will swoop down and scrape the top of the tower with its talons. Try to move to the side to avoid its scraping attacks. When the bird's head is smacked with the Hammer a few times, its helmet will crack, and its rooster-like comb will now be vulnerable to your sword strikes. After doing enough damage to the bird's head from that point on, it will then fly off and vanish in a puff of smoke. Link will dance around in victory, and our next Heart Container will appear for us to collect.
After the defeat of the Helmaroc King, the spikes barring your way to a ramp leading up to the broken half-ship will be disarmed. Go up the ramp and enter the half-ship, where you'll enter a cutscene where Ganondorf introduces himself and congratulates Link for his reckless courage. Ganondorf laughs as Link gets ready to use his sword, telling the youngster that the Master Sword has served as a key that held the seal over his magic in place, but that now Link has removed the sword, the seal also has been removed. Link charges at Ganondorf with the sword, but he ends up falling before his enemy, who easily swats him away. Ganondorf tells Link that he cannot possibly defeat him with a sword that doesn't sparkle with the power to repel evil. Then as Ganondorf lifts up his own sword to use on Link, Tetra enters the room to protect Link, but ends up captured by Ganondorf, nearly strangling her with one hand. Then the Triforce symbol on his other hand resonates, and Ganondorf smiles, saying that "I have found you, Princess Zelda!" But Ganondorf's discovery is interrupted by two Ritos swooping in to rescue Link and Tetra, and Valoo flutters outside the broken half-ship, consuming it in his fiery breath before he and the two Ritos escape with Link and Tetra.
The Castle Under The Sea
The King of Red Lions meet Valoo and the Ritos at the Tower of the Gods, where Link sees that Tetra is now unconscious. After the three airborne heroes fly off, the portal leading to the castle under the sea opens again, and the sailboat lowers itself to the pool of water outside the castle, where Tetra awakens, wondering where she is. Then the King of Red Lions speaks to Link again, this time through the Pirate's Charm, which offends Tetra, as she was the only one who could communicate to Link through it. He tells Link to bring Tetra into the chamber where he got the Master Sword. Once we have control of Link, have Tetra follow you into the entrance of the castle and then down through the secret passageway underneath the Hero of Time statue into the Master Sword chamber. There Link and Tetra will meet the real spirit behind the King of Red Lions: the ancient King Daphnes Nohansen Hyrule. He tells the two young heroes that this place is the ancient kingdom of Hyrule, which was sealed under the waters that the Goddesses have flooded over. He also notices the triangular pendant that Tetra wears around her neck with a piece missing, and provides her with the missing piece that transforms her appearance into that of a princess, causing a Triforce symbol to appear on her hand. The King of Hyrule now tells her that she is Princess Zelda and that she is the bearer of the Triforce of Wisdom. Ganondorf possesses the Triforce of Power and is now seeking the bearer of the other two Triforce parts so he can gain full power. The king instructs Link to leave Tetra who is now Zelda here in the chamber where she will be safe while they go and awaken the sages that will restore the full power of the Master Sword, in addition to finding the eight broken pieces of the Triforce of Courage which was entrusted to the Hero of Time.