Before life began, before the world had form, three golden goddesses descended upon the chaotic land of Hyrule. They were Din, the goddess of power, Nayru, the goddess of wisdom, and Farore, the goddess of courage. Din, with her strong flaming arms, cultivated the land to create the earth. Nayru poured her wisdom onto the earth to give the spirit of law to the world. Farore's rich soul created all life forms who would uphold the law.
These three great goddesses returned to the heavens, leaving behind the sacred Triforce. Since then, the Triforce has become the basis for Hyrule's providence. Where the Triforce stood became sacred land.
In the vast, deep forest of Hyrule, the Great Deku Tree served as the Guardian Spirit. The children of the forest, the Kokiri, lived with the Great Deku Tree. Each Kokiri had his or her own guardian fairy, except one. His name was Link.
Early one morning, Link was having a nightmare. It was the same nightmare he had every night. During a storm, Link would find himself standing in front of a mysterious castle. A rider on horseback, carrying a girl, would race by. The girl would look at Link as if to say something. Then another rider would appear. This big man clad in black would look down menacingly at Link. Link would then awaken.
Link wakes up to the sounds of a fairy, who happens to be Navi, who has come to him to summon him to the Great Deku Tree. When he arrives, the Deku Tree tells Link that the man in black is going to bring great evil to Hyrule, and that Link must stop him before he does that.
Source: Official 3DS Site