In the beginning of this journey, the appointed royal knight, Link, and Zelda, princess of Hyrule, set out to explore a cavern beneath Hyrule Castle, from which a poisonous substance called "gloom" has been seeping out and causing the people of Hyrule to fall ill. Its in here that they find historical murals depicting the founding of Hyrule and a subsequent conflict known as the Imprisoning War—an ancient battle against the "Demon King", whom sought to rule Hyrule under his evil reign—which Zelda believes to be related to the mysterious Zonai race, an ancient people that she has been studying.

Upon venturing deeper in the cavern, Link and Zelda discover a mummy being restrained by a disembodied arm. In an instant, the mummy awakens and attacks the princess and her knight. In the aftermath of the scuffle, Link's right arm is wounded, and his Master Sword shattered. The sword remnants fall into a portal. Hyrule Castle is then raised into the sky, while Zelda falls into the depths below; as Link tries to catch her, she vanishes along with a mysterious glimmering artifact. Link is rescued by the disembodied arm, awakening later on the Great Sky Island to find that it replaced his previously damaged limb.

Here on The Great Sky Island, Link meets the spirit of Rauru, part of the Zonai race and the source of his new arm, who helps him traverse the floating island, until he eventually skydives back to the surface of Hyrule below him. Link then learns that the event in the cavern, known as the Upheaval, has wrought chaos upon Hyrule, and he sets out to investigate reports of strange phenomena throughout the kingdom involving the gloom.

Link ventures into an ancient Zonai temples after reuniting with his allies; Sidon, the prince of the Zora; Tulin, a young Rito archer and son of Teba, a past ally of Link's; Yunobo, a Goron, who is a newly elected president of the YunoboCo mining company; and Riju, the young chief of the Gerudo. After defeating the various monsters that have taken over temples scattered scross the land, the group finds artifacts called secret stones and meet the spirits of ancient sages, who appoint Link's allies as their successors and pass down their and special abilities that will help Link along his journey.

After numerous reported sightings of Zelda throughout Hyrule, Link finally catches up to her at Hyrule Castle, where she reveals herself to be an illusion created by Phantom Ganon, a servant of the Demon King, Ganondorf, whom is actually the mummy Link previously encountered.

Link must then set out to assemble a mechanical body for her spirit to inhabit to better reach her and speak of Hyrule's history. Through Mineru, the ancient sages, and Dragon's Tears (small glowing stones scattered across hyrule that reveal integral memories to the mystery of where Zelda has gone), Link finally learns of Zelda's fate.

The artifact Zelda encountered when she made her fall through the chasm was a secret stone that transported her to the distant past, where she meets Rauru, Hyrule's first king, and Sonia, its first queen. She quickly bonded with the royal couple, seeing them as parental figures she never had in previous years. Here, while Zelda is in the past, Ganondorf tragically murders Sonia to take hold of her precious secret stone and uses its power to become the Demon King.

In response, Rauru appoints his older sister Mineru, Zelda, and the leaders of the Zora, Rito, Gorons, and Gerudo as powerful sages. With the help of everyone during an intense and devastating battle, Ganondorf was weakened but unfortunately, still on the prowl. To make sure that Ganondorf could no longer spread his hate, King Rauru sacrifices himself, using his power to encase the two into stone to seal the demon king away. However, it is said that this seal will not last forever. After this battle, princess Zelda, still in the past, receives the shattered Master Sword from the future and tasks the sages with aiding Link to defeat the Demon king, once he ineveitably reawakens.

It is said that the irreplaceable Master Sword can only be healed with time. But, there is no possible way to assure that Link will safely recieve his precious sword if its left to rot somewhere in Hyrule until present day. Because of this, Zelda decides to makes the sacrifice of a lifetime; she swallows her secret stone and undergoes the process of "dragonification"; when a secret stone is swallowed by its user, they will transform into an immortal dragon. This process can never be reversed. Zelda immediately begins bursting with rays of light, tears streaming down her face, as she transforms into a beastly light dragon, flying through the air. She keeps the sword on the crest of her head, forever looping around Hyrule in the sky.

Back in the the present, after ridding the Great Deku Tree from gloom in Korok Forest, Link finally puts the pieces together; his princess sacrificed herself to protect his sword, and he must go retrive it. He finds her soraing in the sky, and gracefully removed the repaired sword encased in her head. Link then goesbelow Hyrule Castle to confront Ganondorf, in a place called the Depths.

With aid from Sidon, Tulin, Yunobo, Riju, and Mineru, Link battles an army of monsters before engaging in combat with Ganondorf himself. Nearing defeat, Ganondorf swallows his secret stone, becoming a Demon Dragon in a final attempt to kill Link. With help from the Light Dragon, aka Zelda, Link uses the newly repaired Master Sword to shatter the Demon Dragon's secret stone, killing him instantly.

After the battle, the ancient spirits of Rauru and Sonia return and do something unheard of; help Link return Zelda to her normal self. They also use their power to restore his right arm before fading away; he and Zelda fall to the surface in eachothers arms, where they finally reunite.

Some time later, on the Great Sky Island, The spirit of Mineru bids farewell to Zelda and Link before fading away, while the new sages vow to protect Hyrule going forward.