A Tragic Origin (Skyward Sword/Ocarina of Time) -
Ganondorf was born into the Gerudo tribe of female thieves and raised by a surrogate mother/witch, Twinrova to be their king. The Gerudos themselves are cruel and dangerous warriors and no doubt raised Ganondorf to replicate these very characteristics. It is assumed that, during the period when no male king is present, that Gerudos reproduce by using Hylian soldiers thus Ganondorf, along with many other Gerudos born around the same time, has Hylian blood in him.
The desire to take is a trait given to him by his Gerudo blood, but his desire for power is something engraved into his fate. At the end of Skyward Sword when Link defeats Demise, it is stated that an incarnation of him will follow the descendants of both Link and Zelda and torture the inhabitants of the land. This is an obvious reference to the constant threats of Ganon, however, it should not be assumed that only Link and Zelda's descendants were punished for the killing of Demise. There was another hero that had just as much to do with Demise's fall as the heroes.
A Power-Hungry Fool (Ocarina of Time) -
The first chronological appearance of Ganondorf is in The Legend of Zelda's first venture into 3D. Ganondorf is the king of a tribe of desert bandits known as the Gerudo. Every one hundred years a male is born into the Gerudo tribe, which comprises nothing but female bandits, and becomes their king. After the Hyrulean Civil War, Ganondorf creates a relationship between the Hylians and the Gerudos. By gaining the trust of the King of Hyrule, he enters the Sacred Realm through the Temple of Time (previously opened by Young Link's possession of the Sacred Stones) and takes the Triforce of Power. Using his piece of the Triforce and his army of Gerudos, Ganondorf easily usurps the Kingdom of Hyrule. He remains in power for seven years until Link awakens to defeat Ganondorf and banish all evil from Hyrule.
A Humbled King (Wind Waker) -
Ages after the events of Ocarina of Time, Ganon escapes the Sacred Realm and wreaks havoc on Hyrule but unfortunately, no hero came about this time, leaving the Sages to fend off the evil threat by flooding Hyrule and everything in it. The descendants of these Ancient Hylians took to the mountaintops (now islands) and began a new era. The history of the once great kingdom became nothing but a legend.
"It can only be called fate. . . . That here. I would again gather the three with the crests."
An Unrealized Destiny (Twilight Princess) -
After Ganon was defeated, Princess Zelda sent the Hero of Time back to relive his childhood. When Young Link met the young Zelda, he warned her of what Ganondorf had planned to do which confirmed her own suspicions. Zelda informed the King, which led to a Hylian invasion of the Gerudo Desert and the capture of the Gerudo King. The Hylian army desecrated the Gerudo's holy Spirit Temple and modified it into a makeshift prison to house all of the desert thieves and dubbed it The Arbiter's Grounds.
After one hundred years in the Twilight Realm, Ganondorf, convinces Zant, who had been refused the Twili throne by Midna, to take over the light world and usurp the Kingdom of Hyrule. With the castle in his possession, Ganondorf now had the means of making the Triforce whole and realizing his true fate.
An Undying Evil (A Link to the Past/Legend of Zelda/Adventure of Link) -
In a timeline where Ganon defeats the Hero of Time, Ganondorf fulfills his fate given to him by Demise. Transformed into Ganon, he returns time and time again to wreak havoc on Hyrule. Ganondorf, the Gerudo King, would be forgotten through time and the King of Evil, Ganon, would take his place in the winds of the declining kingdom for the rest of time.