It's a direct sequel to the Minish Cap that expounds more on the backstory of Four Swords and Four Swords Adventures, and also sets up one of the characters in the original fic I'm planning.
Vaati attacks Hyrule Castle with an army so he can claim his revenge against Link and Zelda for defeating him. They flee to the Tower of Winds, which Vaati reveals was his plan all along; he knocks Link off the side, kills Zelda and claims the Wind Element and with it the power of the winds. Link is carried to the Royal Valley by Zeffa, where the ghost of King Gustaf reveals that he was the Hero of Men. He tells Link that Vaati doesn't understand the power he wields and that if he can strip Vaati of his sorcerous powers, he'll lose face and won't be able to control the wind any more, then he can be defeated and sealed within the Four Sword, but only with the help of Zelda and the Light Force. Link journeys far south of Hyrule to learn the Dragon Song and summon a huge dragon called Lakityrm to attack the Tower of Winds and get Zelda's body back, then with the aid of the Three Great Fairies and Syrup the Witch, he brews a potion to bring her back to life. Then he journeys to the Gerudo Desert to get the Null Bow, with which he can strip Vaati of his powers, and the Binding Spell, with which he can seal him inside the Four Sword. There, he defeats one of the ancient deities of Hyrule, the Corrupting Dark, and seals him inside the Trident of Power. He returns to find Zelda fully recovered, the two attack the Tower of Winds and defeat Vaati in a climactic showdown. They seal the Four Sword away in the Four Sword Sanctuary and all is well again.
The story explains why in the Minish Cap, Vaati is a sorcerer, but in FS and FSA, he's a wind mage, and also why the Trident of Power corrupted Ganondorf into Ganon in the backstroy of FSA.