“My country lay within a vast desert. When the sun rose into the sky, a burning wind punished my lands, searing the world. And when the moon climbed into the dark of night, a frigid gale pierced our homes. No matter when it came the wind carried the same thing... death. But the winds that blew across the green fields of Hyrule brought something other than suffering and ruin. I coveted that wind, I suppose. It can only be called fate... That here, I would again gather the three with the crests... That I should lay my hand on that which grants the wishes of the beholder... That when power, wisdom, and courage come together, the gods would have no choice but to come down... The power of the gods… The Triforce! He who touches it will have whatever he desires granted! Already the crest of wisdom is mine. All that remains… Do not fear. I will not kill you. I merely have need of the power that dwells within you. Now! Let us put an end to that which binds us together!”
Every one hundred years, the all-female Gerudo tribe gives birth to a male who is recognized as their king. As Demise promised Link and Zelda upon his defeat at the end of Skyward Sword, there would always be an incarnation of his hatred to walk upon the Earth. That revival comes in the form of Ganondorf, king of the Gerudo, usurper of Hyrule, and (as far as I'm concerned) the single greatest villain in video game history.
In A Link to the Past, Ganon is referred to as having once been a man, before he discovered a greater power that allowed him to transform into the powerful beast. As Ocarina of Time is the first game in the timeline confirmed to follow Skyward Sword, we can only assume that to be the first appearance of Ganondorf. As he makes clear to Link, Ganondorf intends to overthrow the king of Hyrule and command the power of the Triforce as his own. When Link removes the Master Sword from its pedestal in the Temple of Time, he opens the Sacred Realm, which allows Ganondorf to steal the Triforce of Power. He then uses it to reshape the kingdom as he sees fit.
During the seven years that followed, Link spent his time asleep in the Sacred Realm, while Zelda evaded Ganondorf’s grasp by taking on the guise of Sheik. Link eventually helped all six of the sages awaken, and they in turn helped him to forge a path to Hyrule castle, but not before Zelda revealed her true identity and was captured by Ganondorf. The only one capable of stopping Ganondorf, Link proceeded to his castle and ascended to find Ganondorf waiting for him. With all three pieces of the Triforce in one place, Ganondorf intended to kill Link, his only remaining opponent, and claim the Triforce of Courage.
Reflecting his own dark magic back at him, Link was able to defeat Ganondorf, but the Gerudo King used the Triforce of Power to transform himself into the beast Ganon. While Link lost his advantage temporarily, he was able to retrieve the Master Sword and, with the help of the sages, sealed Ganondorf away.
There are a number of theories regarding how the Legend of Zelda timeline progresses. For the sake of avoiding debate, I will simply be covering Ganondorf’s actions in the other two titles he appeared. In Twilight Princess, Ganondorf was recognized as a threat to the kingdom and the sages attempted to execute him. They soon realized the extent of his power, however, as a blade to the chest did little harm. Ganondorf killed the sage of water, and – seeing the severity of the situation – the other sages sealed him away in the Twilight Realm.
Once there, Ganondorf took advantage of Zant, leading him to believe that he was some kind of a God. He granted Zant some of his powers – enough to travel to Hyrule and shroud portions of it in Twilight, but nothing comparable to the strength of the Gerudo King himself. After Zant’s defeat, Link and Midna stormed Hyrule Castle to find Ganondorf had assumed the throne. Eventually they were able to free Zelda from his control, and Link killed him, driving the Master Sword through his preexisting wound.
In The Wind Waker, the same Ganondorf Link sealed away in Ocarina of Time has found a way out of the Sacred Realm. When he planned a second conquest of Hyrule, there was no hero to stop him, and so the Goddesses flooded the realm, creating the Great Ocean. Hundreds of years later, there are but a few who remain that know even a little about Hyrule, one of them being the King of Red Lions, talking boat and travelling companion of this era's Link. While the two set out to face the challenges of the tower of the Gods and retrieve the pieces of the shattered Triforce of Courage, Ganondorf has already sent his minions forth to kill the last two remaining sages, Laruto and Fado. He's also gathered quite a collection of young girls with pointed ears, hoping that one of them might be the descendant of Princess Zelda.
Around the midway point of his journeys, Link finds the Master Sword beneath Hyrule Castle. But the blade of evil's bane has lost all its power, forcing Link to tackle two more dungeons to return it to its former glory. At the same time, most of Ganondorf's power was sealed beneath the pedestal of the Master Sword. With it removed, Ganondorf is once again able to assume his Ganon form, as well as his superhuman strength. When Link ventures to his tower to face him, Ganondorf already has Tetra/Zelda, and makes quick work of Link, beating him until he is nearly unconscious. The three pieces of the Triforce resonate, and Ganondorf relays his wishes to the Goddess.
Unfortunately for him, the King of Red Lions (aka the King of Hyrule) intervenes, touching the Triforce first and bringing his own wish to wash away Hyrule to fruition. Outraged, Ganondorf then faces Link and Tetra one final time, intent on taking them down with him as the ocean floods in all around. Link ultimately prevails, with help from Tetra's carefully-aimed light arrows, and drives the Master Sword into Ganondorf's skull.
In Ocarina of Time, Ganondorf is at his most malicious, sending forth every imaginable enemy to hinder Link's progress and attempting to kill the Deku Tree, Jabu Jabu, the Gorons, and the Zoras. His hatred and anger are displayed quite prominently as well, through his rage after his castle collapses. In Twilight Princess, he takes on the role of puppeteer, hoping it will be too late for the people of Hyrule by the time they realize Zant is not the true threat. And in The Wind Waker, Ganondorf shows maturation since his time in the Sacred Realm. His plan is much more carefully laid out, and he nearly succeeds. When it's all said and done, though, Ganondorf is still as vengeful as ever, throwing everything he has at Link and Zelda. Despite how many times Link defeats him, Ganondorf and Ganon will continue to return, just as Demise said he would, bringing pure hatred wherever he goes. There aren't many video game villains that can be both as iconic and as enduring as Ganondorf. And those are the reasons he ranks as the greatest villain of all time.
I have two favorite themes for Ganondorf. The first is from Ocarina of Time, when Link parries magic spheres back at him. The second is the sword duel with Ganondorf at the end of The Wind Waker, and both of these easily fall among the most atmospheric and epic final boss battles I have ever played through in any video game.