…Vanquished to the Dark Realm, Ganon has lain silent for decades, quietly contemplating the countless setbacks he has endured. Through all the battles, his biggest foe was not his nemesis Link, but rather the Master Sword, the mythical blade forged alongside the Triforce by the Goddesses themselves at the beginning of time. Without this sword, Link would be no match for Ganon's strength, and thus his latest plan was born…
PRESENT DAY: Elder Link has observed a quiet life rebuilding Hyrule. As a servant of Zelda, as well as her closest friend, he has overseen the development of just governances to regulate trade, as well as the training of a new quiver of Hylian knights to protect the land in his stead. During the annual celebratory feast of Midwinter's Eve, Link and Zelda are informed of strange disturbances in the land, time-shifting vortices that, "…shimmer in the air, and spoil crops".[DM1] The next day, desiring an adventure similar to those of his younger days, Link selects the most promising apprentice from the Hylian Forge, Destin, to accompany him on his investigation of the 'deathly shimmers'. The pair travel throughout the land, to each of the areas of Hyrule, to explore these rumors.
– THE DESERT OF MYSTERY (Lanayru Desert): Link discovers that the vortex appears randomly at one of three main areas: the Gorge, the Mines, and the Caves.
– LAKE HYLIA (Lake Floria inside Faron Woods): Link's apprentice, Destin, correctly surmises that the vortex is appearing in the center of the lake, and in the Deep Woods (near the Faerie Cave).
– DEATH MOUNTAIN (Eldin Volcano): Link discovers the vortex at the summit, flickering between light and the Twilight Realm, revealing the beastly form of Ganon! Instantly, Link strikes at his foe with the Master Sword, but the blade is shattered upon contact with the time vortex. After the vortex vanishes, Link and Destin postulate that Ganon could only have achieved time manipulation by a single means: the Ocarina of Time.
Back at Hyrule Castle, Link and Destin discover that the Ocarina is missing! It is then that Zelda breaks down into tears, and admits that she has been having recurring nightmares about Ganon's return. Yet, the other night, she suddenly awoke at the summit of Death Mountain, just in time to watch Ganon disappear into a shimmering vortex with the Ocarina. Zelda can only assume that she was coerced into stealing the Ocarina for Ganon.[DM2] Feeling responsible, Zelda informs Link that he must pursue Ganon through the Temple of Time. Link forgives Zelda, but informs her that they cannot chase Ganon because the Master Sword was the only way to open the temporal gateway.
Yet, Zelda informs Link that the Hylian Goddess was imbued with a special power that she was to reserve only for the most desperate moment: she can open the Time Gate, but only once, and afterward would be encased in dimensional crystal for all time. [DM3] Determined to defeat Ganon, and restore the Ocarina, Link and Destin strap on their armor, and head with Zelda to the only place left to chase Ganon: The Temple of Time.
At the Temple, Zelda informs Link and Destin to look past their own desires, and focus on that which must be accomplished. Zelda does the same herself, and the Time Gate flickers into existence just as she is encased in iridescent crystal. Heartbroken, but committed, Link leads the way through time…
Throughout their journey, Link and Destin must travel through each of the major realms visited in the past, such as the Twilight Realm, and Skyloft, defeating Ganon with the help of local wisdom, and various weapons. Yet, in the end, they reach Ganon too late, and he successfully shatters the Master Sword moments after it has been created.
Destin feels hopeless, and Ganon is ecstatic with victory, but Link informs him that the power held within the Master Sword was not due to Fi, or the Goddesses, but rather Link's spirit. All along, across the many battles, the ultimate lesson was to believe in himself. As such, Link doesn't need the sword to defeat Ganon, and subsequently challenges his foe to one last fight, with no weapons, only raw strength.
Ganon accepts, and Link ultimately gets the upper hand, but he sacrifices himself in order to save Destin. After Link's death, Destin kills Ganon, once in the real world, and once in the Dark Realm. Afterward, the spirits of Link and Zelda appear, and inform Destin that the Legend of Link is eternal, and it provides hope when all seems lost. Soon, Destin is guided by the spirits back to Skyloft, to embody the Legend of Link once again, to relive the trials, in order to provide light when darkness comes. Satisfied, Link and Zelda disappear forever into the light…
[DM1]As reported by some of the villagers.
[DM2]Ganon is an inter-dimensional being, not an inter-temporal being. However, he cannot appear within Hyrule Castle because it is guarded by the Triforce. Thus, he enslaved Zelda by terrorizing her dreams, and forced her to sleepwalk, steal the Ocarina, and travel to Death Mountain.
At this point, Link concludes that the vortex appears due to Ganon's attempt at creating a time portal by playing the Ocarina. However, due to his lack of musical skill, Ganon has yet to focus his intentions on his desired location, wherever that may be… He will, undoubtedly, become more skilled over time, and thus he must be pursued without hesitation.
[DM3]Of course, Link tries to dissuade her, but he knows there this is the only way. Defeating Ganon for the sake of everyone else is more important than his love for Zelda.