Spoilers follow, so please read with caution!
Skyward Sword is the very first Zelda game – set before Ocarina of Time or any of the other games. In Skyward Sword, Link is a young boy living a land above the clouds called Skyloft. Skyloft came into existence long ago, when a fierce war in the world forced the goddess of the land to gather all surviving humans onto a piece of land and send it up into the sky in order to protect them. Eventually the evil forces on the land below were sealed away, and over time the citizens of Skyloft all but forgot that there was a world below, however they remember the goddess and honor her in certain traditions.
The unique situation of living in the clouds caused Skyloft residents to bond with Loftwings, giant birds which not only allow humans to ride them but act as a person’s guardian. Link is a student at the Knight Academy and he wins the Wing Ceremony, an annual event that consists of a race and ceremony for the winner. As winner of the race, Link completes the ceremony with his childhood friend, Zelda. Afterwards they go flying together, when all of a sudden a tornado appears and Zelda falls through the clouds. Link is knocked unconscious and awakens back in Skyloft. While in bed at night, a mysterious spirit beckons to him and leads him to the goddess statue in Skyloft, where a sword rests inside. There, she informs Link that not only Zelda is still alive, but that he is the chosen hero of the goddess who must embark on a journey. The spirit introduces herself as Fi, explaining that she is the spirit who resides in the sword and that Link must use this sword – the Goddess Sword – on his journey. Link takes the sword, and Fi opens up a portal through the clouds to the world below.
Link sets out looking for Zelda and spends the first part of his journey following her to temples. He encounters Lord Ghirahim, a demon who is also pursuing Zelda. Fortunately for Link, Ghirahim initially doesn’t think him much of a threat and is focused on his own goal of capturing Zelda in order to use her to revive his master. Link finally catches up to Zelda as she is about the enter Gate of Time, but before she can explain to Link what she’s doing, Ghirahim attacks. Link holds him back long enough to make sure that Zelda and her companion Impa can enter, but Impa destroys the gate to ensure that Ghirahim can’t follow them.
Link discovers a second Gate of Time at another location, but initially he cannot use it as it is inactive. When he unveils the gate, a nearby seal holding a fearsome beast known as The Imprisoned is weakened, and the beast tries to escape. Link manages to seal it back into its prison, and then sets off to find the three sacred flames he needs to empower his sword in order to activate the Gate of Time. His search for the flames takes him through trials and then more dungeons. After he has gathered all of the flames, he returns to the Gate of Time. As he is about to activate it, the seal on The Imprisoned weakens again, and Link has to seal him back in. He then activates the Gate of Time and enters to find himself in the distant past, where he meets Zelda at last.
Zelda explains to Link that they are standing in a time shortly after the goddess sent Skyloft upwards and sealed away the evil force. The evil force is what Link knows as The Imprisoned, but this is only the shadow of a great demon called Demise, the master whom Ghirahim is seeking to revive. Zelda reveals that she is the mortal reincarnation of the goddess, who has taken mortal form in order to stop Demise for good. Her plan is to enter into a deep sleep in this time in order to use her power to keep Demise’s seal strong over the years, while her chosen hero – Link – must find the mystical Triforce and use it to destroy him. Before she goes to sleep, she empowers Link’s sword, transforming it into the Master Sword, and gives Link the clue that the Triforce is hidden somewhere in Skyloft as when she was the goddess she sent it there with the people to keep it out of Demise’s hands.
Link returns to his own time and to Skyloft. As the memory of the Triforce is but a legend among the people there, he seeks out the great sky spirit, Levias, for help. Levias tells him that if he learns the Song of the Hero it will lead the way to the Triforce. Link seeks out three dragons to learn three parts of the song from, and learns the final part from Levias himself. Upon completing the song, Link heads back to Skyloft where he indeed discovers the Triforce and uses its power to destroy Demise. Fi confirms that Demise’s existence has been eradicated completely, and Zelda awakens from her sleep. Their celebrations are cut short, however, when Ghirahim appears once more. Although upset that Demise has been destroyed, he realises that the demon king is still alive in the past, so he kidnaps Zelda and takes her through the Gate of Time to the past. Link quickly follows, and fights off the hordes of monsters that Ghirahim summons to distract or even defeat Link so that he can perform the ritual to revive Demise using Zelda’s soul. Upon reaching Ghirahim, he fights the demon lord who promises that he won’t disregard Link any more. When Link wins, he triumphantly declares that their fight took up enough time for the ritual to be completed, and Demise is revived.
Glad to be free after so many years, Demise declares that he will take over the world. He is used to humans fleeing from his presence, and is surprised when Link not only does not do this, but draws his blade against him. Amused, Demise challenges Link to a duel and retreats to another realm. There is still time before Zelda’s soul is fully absorbed, and so Link follows him. After a tough battle, Link prevails. Before he dies, Demise tells Link that his hatred will live on and will be reborn to constantly pursue the Triforce and those with the blood of the goddess and the chosen hero. His spirit is then sealed within the Master Sword. Zelda and the world below are safe, and Zelda decides that she wants to live there on the surface.