This is the first game in the Unified Timeline before The Legend of Zelda: Ocarina of Time caused the timeline split. The events of the game take place in Skyloft and the surface. Although many places are similar to known landmarks in other Zelda installments most are unconfirmed. Because this is the earliest setting of any Legend of Zelda game it is likely that these places are the originals.
Centuries prior to the events of the game, the goddess Hylia, protector of the Triforce, fought a great evil threatening to destroy the entire world; to protect the race of her people from being annihilated, she sent them far away, up above the clouds. Together with the remaining races of the world, Hylia battled the evil forces of darkness, and ultimately managed to seal the evil power away. The legend of the goddess passed down from generation to generation of the Hylians who came to live in Skyloft, the center of their civilization in The Sky.
Centuries later, Link is introduced as a young resident of Skyloft and a student of the Knight Academy; the goal of any Knight Academy student is to become one of the Knights of Skyloft, airborne protectors of the people residing in The Sky. All denizens of Skyloft have their own Loftwing, being mighty birds that carry them on their backs. Link, a skilled bird-rider in his own right, owns a rare Crimson Loftwing; as the game begins, the time of the traditional Wing Ceremony is at hand. The winner of the ceremony will be promoted to senior rank, and given a gift by Zelda, a childhood friend of Link's and daughter ofGaepora, the academy Headmaster.
Groose, Link's pompous and conceited classmate, attempts to spoil Link's winning chances by kidnapping his Loftwing, hoping the ceremony will go on without him. However, the Wing Ceremony is delayed so that Link may find his missing bird; in a vision, Link sees his Loftwing sealed inside a small cave on the underside of the island, beyond the Waterfall Cave. Utilizing a Practice Sword given to him by Eagus, Link enters the Waterfall Cave and releases his Loftwing from captivity. Despite the best efforts of Groose and his lackeys Cawlin andStrich to stop him during the actual ceremonial race, Link retrieves the Bird Statuette and is made the winner.
The elated Link meets Zelda atop the Statue of the Goddess, where he receives Zelda's self-made Sailclothand masters using it; afterwards, the two embark on a flight together. During their flight, however, a giant tornado appears out of nowhere and throws Zelda and Link off of their Loftwings, sending Zelda straight to theland below the clouds and knocking Link unconscious. Link dreams of a mysterious blue figure and his parting with Zelda before waking up in his bed to see Gaepora standing in his room. Upon being asked, he informs Gaepora what has happened to Zelda and is left to rest until morning when it is possible to search for her using his Loftwing.
Soon after Gaepora leaves, Link hears a mysterious sound and wanders out of his room to find the same blue figure from his dream. He follows it to the Isle of the Goddess, where it opens a hidden doorway leading to a hidden chamber inside the statue. The figure introduces itself as Fi, a spirit residing within the Goddess Sword enshrined there; Fi tells Link that he is the one chosen by the goddess to complete the goddess's task. Link withdraws the Goddess Sword from its pedestal, and focuses power in the blade, unleashing a magical energy that activates a Goddess Crest found nearby. This, in turn, activates the fragmented tablet nearby, opening a path through the Cloud Barrier leading to a region of The Surface, where Fi suspects Zelda may be found. Link sets out on this momentous task; for his adventure, he is given a knight's uniform. Link takes to the skies and lands at the shimmering beacon created by the Ancient Tablet.
Link arrives in the Sealed Grounds, at the bottom of which he finds an ancient seal. In the nearby temple, he meets a mysterious Old Woman who safeguards the seal. She tells Link that Zelda has already passed through, and that he must follow her into Faron Woods. Link passes through the Sealed Temple to Faron Woods, where he uses the Goddess Sword's powers of dowsing for targets based on their energy signature to continue his search for Zelda. While in the Woods, he encounters the Kikwis, a race of herbivorous creatures native to the forest. Due to the recent monster infestation, many Kikwi have gone into hiding; the Kikwi elder,Bucha, asks Link to find them for him. After he does so, he receives a Slingshot that allows him to lower a hanging vine leading deep into the woods, following Zelda's trail to the Skyview Temple.
After braving the many trials of the temple, Link is confronted by a mysterious being that has been shadowing him. He reveals himself to be Ghirahim, Demon Lord of the monsters inhabiting The Surface. The condescending, scheming Demon Lord does not consider Link a threat, even after he is bested in a duel, and leaves promising they will meet again. Defeating Ghirahim opens the door to the spring found at the back of the temple, but Zelda has already come and gone. Link activates another Goddess Crest, opening another pathway through the Cloud Barrier. Link's next destination turns out to be the malevolent volcanic region of Eldin.
Upon his arrival, he meets the native Mogma, who inform him of an unidentified person who passed through the area not long prior to Link's coming. After navigating the river of lava, Link meets the aforementioned person, who introduces herself as one of the Sheikah and urges Link to hurry to the Temple to save Zelda. Link scales the volcanic mountain and enters theEarth Temple. After defeating Ghirahim's servant Scaldera, Link catches up with Zelda and the Sheikah from before. However, their reunion is brief as Zelda must continue her own journey of self-purification; the Sheikah stays a moment longer to chastise Link for being late and failing to save Zelda, and states that the Goddess may have made a mistake in choosing him as the hero. Tasking Link with summoning a shred of courage to face the trials ahead, she leaves him behind with more unanswered questions. He receives the Amber Tablet, granting him access to the next area to which he must travel.
In Lanayru Desert, Link uses the Timeshift Stones found in the area to manipulate the flow of time around him. This allows him to navigate the area and interact with its mechanisms and the area's sole inhabitants, theAncient Robots, as they were hundred of years before they succumbed to the destructive powers of the desert's harsh climate. Zelda's trail leads to the Temple of Time found in the western desert, but he is not able to enter the temple itself due to his path being blocked. Link navigates the Lanayru Mining Facility, which turns out to be a secret pathway to the Temple of Time. He manages to catch up to Zelda and the Sheikah at the temple; however, their reunion is interrupted again when Ghirahim attacks. Zelda and the Sheikah manage to escape into a Gate of Time before it is destroyed, preventing Ghirahim from reaching them. Before Zelda left, however, she gives Link the Goddess's Harp, a magical instrument.
With Zelda beyond his reach, Link returns to the Sealed Temple; however, as he leaps off his Loftwing to prepare for landing, Groose appears and causes them both to come crashing to the ground. Groose has set off on his own to rescue Zelda, and goes with Link to ask the advice of the Old Woman. She identifies the mysterious Sheikah as being Impa, one charged with guarding Zelda on her journey of self-discovery. Teaching Link to play the Ballad of the Goddess, the Old Woman summons forth another Gate of Time leading to the past in which Zelda and Impa are now found; however, the gate can only be activated when the Goddess Sword has been infused with three Sacred Flames, entrusted to Three Dragonsby the goddess herself, that allow its power to grow. However, the temples these flames are found in can be entered only if the chosen hero undergoes three trials of spiritual growth. To perform these trials, the hero must first learn a specific song for each region, which will lead him to the location where his trial begins. As Link and the Old Woman talk, however, the seal breaks, and the creature it had sealed away, known as The Imprisoned, is able to escape. Link manages to stop it from destroying the temple, and re-seals it, though the Old Woman warns him it will return. Groose realizes that he is out of his depth, but is told that he has his own part to play in the events to follow, and remains with the Old Woman, whom he affectionately refers to as "Grannie."
Link returns to Skyloft to ask Gaepora about the lyrics to the "Ballad of the Goddess", a song that holds a clue as to the location of the Isle of Songs. The lyrics deal, in a cryptic fashion, with the Light Tower found in Skyloft. Link deduces that the tower can be activated if two windmills found around Skyloft are activated; however, according to Jakamar, one of the windmills is missing a mechanism allowing it to function. Link searches for the missing pinwheel, and finds it in the Eldin region. Enlisting the aid of LD-301S Scrapper, one of the Ancient Robots, Link brings it back to Skyloft, and Jakamar repairs the windmill. Atop the Light Tower, Link plays the "Ballad of the Goddess", causing a beam of light to appear which opens a pathway into the Thunderhead and leads directly to the Isle of Songs. After completing the puzzle granting entry into the central tower on the Isle of Songs, Link learns the first of the three songs, "Farore's Courage".
Link returns to Faron Woods in search for his trial, and eventually finds his way into one of the Silent Realms, into which Fi is unable to follow him. In Silent Realms, Link must gather Tears of the Goddesses in his Spirit Vessel, while avoiding the dreaded Guardians and Watchers found there. Once he has done so, he achieves spiritual growth and is granted a blessed item from the Golden Goddesses; the first of these is the Water Dragon's Scale, allowing him to dive into the large tree found in the middle of woods. Atop the tree, Link finds the Kikwi elder Yerbal, who provides him with information on how to enter Lake Floria. One of the Parella native to the lake guides him to the Water Dragon, Faron, whose power has been diminished as a result of her fight against Ghirahim's hordes. To test the hero, Faron sends him on a quest to retrieve Sacred Water from the Skyview Temple, which has been repopulated by new enemies. Upon returning with the water, Link empties it into the basin in which Faron rests, restoring her to full strength. To thank him, she opens the way to the Ancient Cistern, wherein Link finds Farore's Flame, which transforms the Goddess Sword into the Goddess Longsword.
Link returns to the Isle of Songs and learns "Nayru's Wisdom", which leads to a Silent Realm in the Lanayru Desert; upon completion, Link receives the Clawshots, allowing him to travel to the Lanayru Sand Sea, where he must search for the Sandship aboard which Nayru's Flame is found. However, the Sandship has been overtaken by LD-002G Scervo and his crew, who are using a mechanism that allows it to remain invisible to the naked eye; after ransacking the pirates' stronghold, Link is able to find an old shipwreck that Fi is able to use for dowsing. Link is able to find and board the ship, and Nayru's Flame transforms the Goddess Longsword into the Goddess Whitesword, with an improved capacity for dowsing.
Lastly, Link learns "Din's Power". After completing Eldin's Silent Realm, he receives the Fireshield Earrings, which protects him against the immense heat of the volcanic mountain, allowing him to venture deeper inside. He finds that the entrance to the Fire Sanctuary that holds Din's Flame is blocked by a huge mechanism that requires Link dowse it with a large container of water. Faron grants Link permission to use her basin for this purpose, and puts out the flames. Within the Fire Sanctuary, Din's Flame transforms the Goddess Sword into the Master Sword.
With the Master Sword in hand, Link returns to the Sealed Temple and activates the Gate of Time, allowing him to venture into the Sealed Temple of the past. Once there, he is finally reunited with Zelda. Unbeknownst to Link, however, Impa has told Zelda about her true origin; she is in fact the reincarnation of the goddess Hylia, who gave up her divine form to safeguard the mythical Triforce. She reveals that The Imprisoned is, in fact, Demise, the Demon King that she, as Hylia, had fought countless years before. She surmises that the only way to truly defeat Demise is to obtain the Triforce, and use its power to wish for Demise's destruction. She unlocks the true power of the Master Sword, giving it the power to repel evil. To reinforce the seal placed on Demise, she must remain behind in the past, sealed inside a crystal, to awaken only when Demise has been destroyed. Link promises to return for her once this is done.
To find the Triforce, Link must learn the "Song of the Hero", known only by Levias, a wise and powerful whale residing in The Sky. However, recently Levias has been acting strangely, attacking anyone who approaches him. Link is able to summon Levias with a vat of his favorite food, Pumpkin Soup, and uses his Loftwing to combat the creature infesting him. Levias returns to normal, and reveals to Link that knowledge of the "Song of the Hero" is divided between himself and the Three Dragons. He teaches Link his part of the song, and Link is free to choose in what order to approach the Three Dragons.
Link learns Faron's part of the song after he gathers several Tadtones scattered throughout Faron Woods, which Faron has flooded to prevent further monster attacks. After gathering them all, Faron returns the forest to normal. Upon arriving at Eldin Volcano, the volcano erupts, and Link is blown off course and rendered unconscious. When he awakens, all his equipment has been taken from him by Bokoblins. Link utilizes stealth and deception in order to reclaim his equipment, and the impressed Fire Dragon, Eldin, teaches him his part of the song.
Upon arriving in Lanayru Desert, Link finds that Lanayru has passed away, and only his skeleton remains. Utilizing the power of a nearby Timeshift Stone, Link is able to travel into the past, where he finds that Lanayru is gravely ill, and unable to sing. Link takes the Life Tree Seedling that an LD-301 robot was planting, which grows intro trees that bear Life Tree Fruit, a powerful cure-all, intending to plant it in a more fitting location than the harsh desert. Link finds the ideal spot in the Sealed Temple, but rather than plant it in the present, he travels into the past through the Gate of Time and plants it there, and the fully-grown tree has grown a Life Tree Fruit upon his return. He takes the fruit to Lanayru, who is revived instantly, and gladly teaches him his part of the song. Link returns to Levias, where he and the Three Dragons perform the complete "Song of the Hero".
Link returns to Skyloft for one last time, and finds the spot where he must play the "Song of the Hero". He travels to a Silent Realm, and after gathering all the Tears of the Goddesses, Link is presented with the Stone of Trials, which leads the way to the resting place of the Triforce. Link places the stone in a bird statue near the waterfall, which reveals Sky Keep to have been hidden underneath the Statue of the Goddess all along. The dungeon contains elements from every one of the game's dungeons. Piece by piece, Link reassembles the Triforce, and once completed, he is transported atop the Statue of the Goddess. Link makes his wish, and the Isle of the Goddess is torn apart from the continent of Skyloft, and sent below the clouds to where it once belonged in the Sealed Grounds. It lands atop Demise's seal, destroying both it and the evil creature which it had sealed once and for all.
Link returns to the Sealed Temple, where Zelda is reawakened from her long slumber. However, Ghirahim appears and takes her away, planning to use her as a vessel to revive the Demon Lord, for in the past, he still lives. Link chases after them into the past, where Link engages in a large-scale battle with Ghirahim's hordes, while Ghirahim is exorcising Zelda's soul from her body to revive his master. After defeating Ghirahim in their last duel, Ghirahim gleefully announces that Link was unsuccessful in stopping his revival of Demise; The Imprisoned appears and absorbs Zelda's soul, returning him to his demonic humanoid form, and restoring Ghirahim to his original form as Demise's sword.
Demise challenges Link into a battle over the Triforce on another plane of existence, and a duel of the fate of the world ensues. Demise is ultimately defeated, but he ominously states that an incarnation of his hatred (and the curse of the Demon Tribe in the original Japanese version) will return in a cycle without end to torment those who share the blood of the goddess and the spirit of the hero, laughing as he dissolves into spiritual energy and is absorbed into the Master Sword. Link returns to the Temple of Hylia to find Zelda restored; as Link, Zelda and Groose celebrate their victory, however, Impa tells them that she cannot go with them, as she belongs in the past. The tearful Zelda gives her one of her bracelets as a token of her appreciation to her.
Upon returning from the past, they discover that the Old Woman is wearing Impa's bracelet, revealing that she had in truth been Impa all along before she disappears, her task complete. Fi says her goodbyes as well, and the Master Sword is enshrined within the Sealed Temple, so that over time, Demise can be truly defeated. In a post-credits scene, Link and Zelda are seen standing atop the Statue of the Goddess; as Groose departs for Skyloft, Zelda then states that she wants to live on the surface world. She then asked what Link intended to do, with Link sweetly smiling at her as the scene moved towards Link and Zelda's Loftwings flying back into the sky, implying that Link chose to stay with Zelda.