Molgera

Molgera is a giant worm like creature that is the boss of the Wind Temple. It is the monster that killed Fado many years ago, and protects a shrine deep within the Wind Temple. Although Molgera likes to hide underground in the sand, waiting for its prey to come close enough within its pit to eat it, Molgera will often leap into the air and attempt to ram its prey below.

Molgera will also send out smaller enemies much like itself to hunt down and attack its foe. To defeat this monster Link had to use his Hookshot to pull its tongue towards him and then cut it up with his sword. He returns as the fourth and final boss in Ganon's Tower, only in black and white to refer the fight as a flashback to Link.

Origin
Hundreds of years prior to The Legend of Zelda: The Wind Waker, the Dark Lord Ganondorf somehow escaped his imprisonment within the tainted Sacred Realm and returned to Hyrule in a red wrath, meaning to make good on his final threat to the Hero of Time that he would make the descendants of his captivators pay for his imprisonment. Since Princess Zelda had sent the Hero of Time back to his childhood, he nor his descendants were present to stop Ganondorf's onslaught. Knowing that the only real threat to him was the very weapon that had last defeated him during the Imprisoning War, the Master Sword, Ganondorf sought to deactivate the sword's true power, the power to repel evil. To this end, Ganondorf used the might of the Triforce of Power he possessed and crafted two horrific monsters, a gigantic Poe named Jalhalla and the great sand-worm Molgera. Ganondorf ordered them to kill the Sages of the Master Sword and take over their respective temples, the Earth Temple and the Wind Temple. While Ganondorf sent Jalhalla to the Earth Temple to kill the Zora Sage of Earth, Laruto, he sent Molgera to kill the Kokiri Sage of Wind, Fado. Molgera led an entire legion of Ganondorf's monsters into the Wind Temple, and while the beasts overwhelmed the temple and infested its chambers, Molgera traveled to the shrine at the heart of the temple, located in a large cylindrical chamber partially filled with sand, and found the small Kokiri Sage there, praying to the Goddesses that the power to repel evil would forever remain within the Master Sword. The gigantic sand worm assaulted the Sage of Wind and murdered him, stealing his soul and taking up residence within Fado's chamber, remaining there to prevent a future Sage of Wind from taking his or her rightful place at the heart of the temple. Fado's magical violin was then passed down his family line over the generations following his death. There the beast would remain until a new Hero would come to investigate the status of the Sage of Wind and the Wind Temple itself.

After the Master Sword's power had been deactivated, Ganondorf continued his assault on the Kingdom of Hyrule, and the people were forced to leave their fate in the hands of the Goddesses since the Hero of Time was now unable to answer their cries for help. In response, the Goddesses instructed the people to take refuge on Hyrule's mountaintops and caused a torrential downpour that flooded the kingdom in a deluge of gargantuan proportions. As the water flooded the kingdom, the land and everyone still down in Hyrule was frozen in time as a magical air chamber was created that preserved the land beneath the vast ocean that was created, which turned Hyrule's mountaintops into islands on the newly-created Great Sea in an event that came to be known as the Great Flood. Ganondorf, his army, and all else still left in the Kingdom of Hyrule were all frozen in place as they were held in stasis with the Master Sword and the Pedestal of Time acting as the key to restoring them and their powers, the sword and pedestal being hidden away in the basement of Hyrule Castle. For centuries following the Great Flood, the Wind Temple, still intact even after the deluge, remained infested by Ganondorf's monsters and the great Protector of the Seal that lurked within the temple's depths.

Coming of the Hero of Winds
Hundreds of years after the Great Flood, Ganondorf, still in possession of the Triforce of Power, was able to unfreeze himself and crafted a portal within his undersea lair down in Hyrule, Ganon's Tower, that led to the island directly above it, namely the Forsaken Fortress, the base of operations for a band of small-time pirates. Ganondorf eliminated these pirates and took over the island, making it his base of operations above the waves of the Great Sea. He then began searching for the descendant of Princess Zelda as well as keeping an eye out for a possible new Hero that could challenge him as the Hero of Time had done. He remained confident however that he could not be defeated, as the Master Sword's evil-banishing power had been deactivated long ago by his own doing. Eventually, a new Hero came to challenge Ganondorf with the Master Sword itself in hand. It was here that Ganondorf revealed the sword's role in keeping his full powers sealed away as well as the fact that it no longer held the power to repel evil. Link attacked Ganondorf regardless, only to fail to place even a scratch on the Dark Lord. As Ganondorf was about to raise one of his own twin blades to strike Link, he was assaulted by the pirate captain Tetra, whom he eventually realized was the new Princess Zelda due to her possession of a fragment of the Triforce of Wisdom on a necklace around her neck. But Link and Zelda were both rescued by Quill, Prince Komali and the great dragon Valoo, who sent Ganondorf's chamber up in flames. Ganondorf was not at all harmed but instead returned to his tower beneath the sea, leaving the Forsaken Fortress empty while he searched frantically for the pair that had escaped him.

Link eventually went in search of the Sages of the Master Sword in order to find out what had happened to the Master Sword's power. He first found Laruto dead by Jalhalla's hand and awakened Laruto's descendant, Medli (who was in possession of her harp) to the fact that she was the new Sage of Earth. After cleansing the Earth Temple of Ganondorf's evil, Link ventured into the Earth Temple's depths and found Jalhalla lurking in Laruto's chamber where the temple's shrine was located. After killing the massive Poe and restoring part of the Master Sword's power with Medli's prayer, Link returned to the surface to discover what became of the Sage of Wind. Traveling to Gale Island, Link was greeted by the spirit of the long-dead Fado, who revealed that he had been murdered by Ganondorf's monster Molgera. Link remembered seeing a violin very much like Fado's earlier in the possession of a Korok named Makar on the Forest Haven, and remembered Makar telling him that the violin had been passed down through his family for generations. Link returned to the Forest Haven and awakened Makar to the knowledge that he was Fado's descendant and the new Sage of Wind by means of the Wind God's Aria. With that, the Hero of Winds took Makar and returned to Gale Island, entering the Wind Temple with the new Sage's help. As the pair worked together to cleanse the temple's vast interior of Ganondorf's monsters, they finally came upon Fado's chamber, and leaving Makar to wait outside, Link proceeded through the chamber's door to confront the monstrosity within. Inside, Link found himself in a large cylindrical chamber and saw the shrine where the Sage's prayers were to be offered in the center of the chamber, surrounded by sand. Link proceeded down into the sand pit to investigate the shrine as there didn't appear to be any threat at first. As soon as he landed in the pit however, the sand began to rise, covering up the shrine and the ground beneath Link's feet began to shake violently, revealing that something large and powerful was lurking beneath the sand. With that, the giant sand worm Molgera, the great Protector of the Seal, erupted out of the sand and flew around the chamber, crashing down into the sand and tunneling beneath the surface. The Hero of Winds battled the enormous sand worm with the aid of his newly-discovered Hookshot found within the temple and used it to grab onto Molgera's weak point, its tongue, so he could strike it with the Master Sword. After several hits in this manner, Molgera rose into the air and roared in great pain as it shriveled up and exploded in a cloud of smoke, leaving Link with a Heart Container and draining enough of the sand out of the chamber to reveal the shrine once again. Makar entered the chamber and played the Wind God's Aria alongside the Hero of Winds, restoring the Master Sword to its former glory and avenging his ancestor's death at the hands of the Protector of the Seal.