After landing, enter the castle that seems to be frozen in time. Go to the middle of the room to see a Triforce symbol. Pull the triangular blocks on the three Triforce triangles, then the blocks will go down the ground and a heavy stone slab will move, giving you access to a staircase. Go down to the basement, then take a few more stairs and draw out the Master Sword, the legendary sword, from its pedestal! By doing so, the castle will come back to life, along with all the enemies inside! You can also take a look at the stained glass panels representing all the seven sages from Ocarina of Time, and go back upstairs to the ground level.
You will now have to defeat all the enemies, along with those on the second floor. The Darknuts (enemies in armour) must be struck in the back. To do so, get close to them quietly or hide behind a block to surprise them. Then, get out of the Castle by using the northern stairs (where you got in). Talk to the King of Red Lions, take out your sail and get into the light.
Now that you own the Master Sword, you are ready to face the Forsaken Fortress again to free your sister Aryll. Have the wind blow north-west and sail towards the fortress (A1). Sail around it to find the main door, blow it up from your ship using a bomb and get inside.
Climb the stairs, get past the room and head towards the huge door on the right. At this moment, Phantom Ganon will attack you. With your sword, deflect his energy balls back at him, then when he is down, quickly attack him with your sword. Do this once or twice more and he will vanish. Open the newly appeared chest and pick up the Skull Hammer.
Then, open the door behind you. Avoid the rats, use the Skull Hammer to smash the stakes and follow the corridor. This time, you can stand against the Moblins, and open the next door. Here, be careful of the Floormaster that will emerge from the ground (if you get caught you will end up back in jail), get on the next corridor and open the next door. Avoid the laser beams, climb on the beds and use the Deku Leaf to cross the gap. Smash the stakes using the Skull Hammer and open the next door. Follow the path, open the door, go ahead and open the huge door leading outside. Climb the stairs around the fortress, then go past the first ledge while doing your best to avoid the searchlights (and, as a result, cannon shots). Throw your Grappling Hook at the wooden part to reach the second ledge. In the courtyard, smash down the wooden post with the Skull Hammer and get inside the room. You'll find Aryll along with the other children. Tetra and her friends will arrive on this and take the children back to their ship, but then Tetra will notice your sword. Everyone leaves, leaving you alone with the huge bird.
Run up the stairs to avoid your enemies, then upon reaching the end of the path, hit the bird's beak with your Skull Hammer to go through. If you fall, you can get back on the path thanks to your Grappling Hook. Keep on going up, the bird will come back and a new fight will begin.
First the bird will fly around the area and land from time to time. When its beak gets stuck while attacking you, use the L lock to hit the beak with your hammer. When it lands legs first, stay back so it doesn't shove you on the spikes surrounding the area. Upon destroying the armour, use the same tactic, but this time with the Master Sword. Finally, pick up the Heart Container, follow the passage and open the door at the fortress' top.
You will end up in front of Ganondorf! After an explanatory cutscene regarding the Triforce, Tetra and you will be saved by the Ritos while Valoo sets Ganondorf's lair on fire. Then, the King of Red Lions will take you to Hyrule Castle.
As the Pirate's Charm is asking you, get inside the castle and go down to the basement. The King of Hyrule will tell you about his realm, about Tetra who is no other but Princess Zelda, and about the Master Sword. Then he will ask you to go back to the Great Sea to restore the surface to normal. Leave the castle, get on board and get into the light. The King of Red Lions will inform you that you need to gather all eight shards of the Triforce of Courage.