Forsaken Fortress

Forsaken Fortress is the first dungeon Link visits in The Wind Waker. It's an ominous island, and most people tend to avoid it. The stone fortress is well-guarded with cannons, searchlights, and hordes of Miniblins, Bokoblins, and Moblins, who patrol and attack any would-be invaders. The Helmaroc King has made his home on the Forsaken Fortress as Ganondorf's servant. It was also the place where Link's sister, Aryll, was held prisoner, along with Mila and Maggie.

Tetra briefly mentions to Link that the fortress previously belonged to another clan of pirates. This may refer to the Gerudo tribe, and would make the Forsaken Fortress the Great Sea version of the Gerudo Fortress. Additionally, the eye and teardrop symbol of the Sheikah tribe can be seen on the ship perched atop the Fortress.

Entrance to the Fortress
The dungeon is located in the far northwest quadrant of the Great Sea, and it is where Ganondorf has constructed his temporary lair by using a portal from Hyrule under the sea. Link is taken there by Tetra and her pirate crew, but he has to visit the place alone with the King of Red Lions in the future.

First Visit
During his first visit, Link is catapulted to the fortress by Tetra and her crew. Upon landing, he loses his sword and is left with only his shield to defend himself. In order to reach the room where Aryll is being held, he must travel to each tower and use Boko Sticks to defeat the Bokoblins operating the searchlights. He must also practice stealth while navigating the fortress, as there are Moblins that patrol the fortress who will throw Link in the fortress jail if spotted. Thankfully, the dim-witted nature of the Moblins allows Link to navigate around without being seen by hiding under Barrels. Once he is outside the room where Aryll is being held, he gets his sword back and fights a shielded Bokoblin. Before Link is able to save his sister and the other girls, the Helmaroc King swoops in, grabs Link with his beak, and brings him before Ganondorf. Ganondorf then tells the bird to discard him, ergo his rescue attempt failed and Link ends up unconscious in the Great Sea.

Second Visit
After Link finds the Master Sword, he pays a second visit to the Fortress, where he confronts Phantom Ganon to gain the Skull Hammer, then the Bokoblins who once more use the searchlights, and finally the dreaded Helmaroc King to rescue his sister and the girls from Windfall Island, with the help of Tetra and the pirates. Although he succeeds in the rescue mission this time, he now fails to defeat Ganondorf because the blade of the evil's bane lost its power, and when Link removed it from the flooded Hyrule in the first place, he lifted the seal that avoided Ganondorf to take control of Hyrule again; because of this, the Fortress is eventually abandoned and the enemies (Ganondorf included) now move to Hyrule. After Link clears the Wind Temple, it's revealed that the Fortress is indeed uninhabited.

As Link has his sword during the second visit, he is able to defend himself and does not need to use stealth as in the first visit. Moblins will now simply attack him, instead of bringing him to the jail. Also, searchlights that are trained on Link will cause Bombs to be fired at him and will also attract Miniblins.

Third Visit (optional)
As Link explores the game's final dungeon, he can find a way to open the warp spot that Ganon and his followers used previously in the Fortress to use it as a shortcut to return to the Great Sea.

Contrary to popular belief, if Link misses the Heart Container gained after defeating Helmaroc King, he still can find it anytime in front of the main wooden gate, near the chest that guarded the Skull Hammer.

Theory
It is interesting to note that along with the other relative locations between some of the islands in The Wind Waker with some of the locations in Ocarina of Time, that the Forsaken Fortress is located in the northwest, just as Gerudo Desert was in Ocarina of Time - both the "home bases" of Ganondorf. The fact that the fortress was inhabited by pirates before Ganondorf's arrival, and in knowing the Gerudo race were pirates themselves, Ganondorf himself leading a gang of thieves before the events of Ocarina of Time, it only emphasizes the possibility that the Forsaken Fortress was the tallest portion of the Gerudo Fortress that survived the Goddesses' flood.

Trivia

 * A modified version of the Sheikah Eye Symbol makes a small appearance near the top of the Forsaken Fortress.
 * This is also one of the only two dungeons without a Warp Jar. The other is Tower of the Gods.
 * This dungeon is unique in that, like Skull Woods in A Link to the Past, it has multiple entrances and exits, given the fact that only the interior is considered to be the dungeon itself (as seen in the Dungeon Map), and the exterior territory belongs to the Great Sea overworld. For the same reason, this fortress is the only dungeon in the game whose boss is fought and defeated outside.
 * The tune that plays as Link is thrown in jail also plays in Four Swords Adventures in the Infiltration of Hyrule Castle when the Links are thrown in jail after being spotted by the searchlights.