"My country was within a desert. The scorching wind under the sun. The dreary wind as the moon climbed… The wind brought death with it…
The wind that blew over Hyrule, brought something other than death. I suppose I sought that wind…"
Born into the Gerudo as the only male in a hundred years, Ganondorf was always destined for greatness. Though few could likely predict just how great he would become. Terrible; but great.
Though it's well documented on how he infiltrated into Hyrule and gained access to the 'power' element of the Triforce, little is known about what happened to him after he was famously defeated by Link and the Sages and banished into the ether.
The result of his loss sent the King of Evil spiralling through empty space and time. Eventually, after summoning enough strength, he managed to rip himself free of the void and find himself in the alternate dimension of Termina. Over the next several years he rebuilt his strength and forces, slowly and surely taking control over the strange Kingdom. Then, when the key moment struck, he led a force of Terminian Gerudo back into Hyrule and seized control.
With Link in Termina, Ganondorf seized the opportunity and took Hyrule by force. With the power of his new 'malice' by his side, he was easily able to take Hyrule Castle and the surrounding areas. He now sits upon the throne, carefully planning out his next move.
The Yiga is Ganondorf's own version of the royal family's 'Sheikah'. Formed from elite soldiers of various origins, they operate largely in the shadows. They infiltrate through disguise and generally cause damage to society by fuelling crime and blackmarket trade.