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Ganondorf's Theme, also known as Agahnim's Theme or Ganon's Theme, is the reoccurring theme used to represent Ganondorf or one of his alternate forms, including Ganon. It first made its appearance in A Link to the Past and has appeared in virtually every single major Zelda game where Ganondorf has appeared.
A Link to the Past
In A Link to the Past the theme plays when Link first meets Agahnim in the Hyrule Castle Tower. It occurs when Agahnim is in the process of sending Princess Zelda to the Dark World. The theme plays once again during the final battle with Ganon.
Ocarina of Time
In Ocarina of Time, the first time the theme plays is when Link is having a nightmare where he dreams of Zelda and Impa escaping from Ganondorf just outside Hyrule Castle Town.
An organ rendition of the theme is played during the final dungeon, Ganon's Castle. It's then revealed than the melody is being played by Ganondorf himself in a church organ.
The Wind Waker
Similarly to Ocarina of Time, a rendition of Ganondorf's theme plays mainly during the final dungeon in the game, Ganon's Tower.
Four Swords Adventures
Ganondorf's theme, again, makes an appearance in the final dungeon, Hyrule Castle, first blended with a minimalistic rendition of Hyrule Castle's theme, and then by itself during the final climb.
During the prologue of Phantom Hourglass, Ganondorf's Theme can be heard when the storyboard frame appears, highlighting Ganondorf's events from The Wind Waker. The theme later appears when Link is traversing through the Fog to reach the Ghost Ship.