Acquiring the Master Sword
Upon entering Hyrule Castle travel all the way down the stairs near the Triforce mark on the ground. The King of Red Lions will speak with you similar to how Tetra did earlier in the game. After speaking with him - simply move the stone blocks near the Triforce mark over the emblem in order to open the passage forward.
Walk down the newly uncovered stairs and continue forward to enter into a cutscene. After the cutscene you need to walk up to the Master Sword and pull it out. This will cause the Hyrule Castle to regain "light" and unfreeze the creatures in the previous room.
Return to the previous room and defeat all of the enemies in order to remove the barriers blocking the exit of the castle. Once the barriers have been removed, exit through the door at the top of the stairs. Speak with King of Red Lions and sail into the bright light to return back to the surface.
Back to the Forsaken Fortress
Set sail northwest towards the Forsaken Fortress located in the top left corner of the Sea Chart. After getting to the Forsaken Fortress, sail around and find the door. Shoot it with the canon in order to open the entrance. Upon entering, the King of Red Lions will give you a short piece of dialog.
Climb up the stairs and run towards the front door. Phantom Ganon will appear and a battle will ensue. Simply hit the energy balls back towards him until it hits - this will stun Phantom Ganon. Now run up and repeatedly strike him with the sword. Repeat this process until Phantom Ganon is defeated.
After defeating Phantom Ganon - the wooden door will become unlocked and a chest will appear containing the Skull Hammer. Now head towards the stairs blocked by an obstacle. Use the Skull Hammer to smash the obstacle and continue up the stairs.
Turn left near the first the opening and enter the door here. Kill the Bokoblin and then use the Deku Leaf to float across the gap. Smash the stake - obstacle - in front of the door and go through it. Follow the hallway and enter the next door.
Float across the gap and then enter the next door. Continue down the hallway and through the next door. Now defeat - or not - the Moblin before entering the double doors at the top of the stairs. Head up the stairs and navigate through the spikes with the Skull Hammer.
Play the Wind's Requiem once you get to the gap and make the wind direction southeast. Use the Deku Leaf to float across the gap. Change the wind direction to southwest at the next gap and use the Deku Leaf to float across the gap. Continue up the stairs and smash the stake in order to open the door.
Go through the door for a cutscene with Link's sister as well as Tetra and the pirates. After the cutscene you need to quickly travel up the path while avoiding any confrontation. Once at the top simply smash the beak of the Helmaroc King to knock him into the water.
Forsaken Fortress Helmaroc King Battle
Climb up the rest of the way and prepare for a battle. Dodge the Helmaroc King's attack until he tries to peak you - getting his beak stuck into the ground. Smash the beak with the Skull Hammer. After five times the armor will break off.
Now wait for the Helmaroc King to once again try to peak you and get its beak stuck in the ground. Attack it with the sword several times to defeat it. Grab the Heart Container and continue up the path and through the door for a cutscene with Ganondorf.
Back to Hyrule Castle
After the cutscene - the King of Red Lions will take both Link and Tetra back to Hyrule Castle. Enter the castle and head back down to where you got the Master Sword. Another cutsene will ensue where Link finds out that he must now return the power to the Master Sword in order to defeat Ganondorf. Return back to King of Red Lions and travel through the portal back up to the sea.
Back to Part 9: Tower of the Gods | Continue to Part 11: Earth Temple