Imprisoning War

The Imprisoning War, also known as The Seven Dark Years, is a seven-year long war vastly affected the entirety of Hyrule with darkness and corruption.

Background
Civil war raged across the various races of Hyrule. In this time of crisis, a Gerudo named Ganondorf came to lay down some negotiations with the King of Hyrule. Eventually, the war died down, and Ganondorf gained the King's trust. In truth, Ganondorf was plotting to ursurp the throne and gain access to the Sacred Realm. In his actions, he plagued the Great Deku Tree with an army of Gohma, Death Mountain with Dodongos, and Lord Jabu-Jabu with Bari to gain the Spiritual Stones which unlock the door to the Realm.

Link, an orphan of the Hyrule Civil War who was raised as a Kokiri, was summoned by the Deku Tree. He was sent inside the tree to dispose of Queen Gohma. He succeeded, but failed to keep the Deku Tree alive. Before death, the tree granted Link the Kokiri Emerald, one of the spiritual stones.

Link made contact with Princess Zelda in Hyrule Castle, who explained the situation. Impa, her nursemaid, guided Link to Death Mountain, where he gained the Goron Ruby from the patriarch of the Goron tribe, Darunia after ridding Dodongo's Cavern of Dodongo creatures. Link gained the Zora's Sapphire from Princess Ruto of the Zora tribe for ridding Jabu-Jabu of the creatures plaguing his organs.

The Great Cataclysm
Ganondorf had assassinated the King and pursued Impa and Zelda on horseback into Hyrule Field. Zelda tossed the last key to opening the Door of Time to the Sacred Realm, the Ocarina of Time, into the moat of Hyrule Castle Town. After a brief confrontation with Ganondorf, Link retrieved the Ocarina and retrieved the Master Sword from its pedestal in the Temple of Time after opening the Door of Time. This action would proclaim Link the Hero of Time and open the portal to the Sacred Realm.

Ganondorf had followed Link into the Temple and used the portal to his advantage. He led an onslaught of the Sacred Realm and hauled the sacred Triforce. Upon this moment, known as the Great Cataclysm, the Triforce reflected the Sacred Realm into his evil soul, which would corrupt the realm into the Dark World. Ganondorf's personality inside this mystical place was crafted into a new body, which is known as Ganon.

War
With this new power, Ganon led an army of monsters into Hyrule. The ancient Hylian Knights, which were sworn to defend the Royal Family, were all but completely wiped out. Hyrule Castle Town was left in ruin. Manifestations of Ganon's evil powers, known as Redead, scavaged the ruins of the town for any survivors. Ganon's forces eventually attacked Hyrule Castle itself, toppling it down and constructing a castle of his own in its place.

His forces, led by a reflection of his body, Phantom Ganon, raided Kokiri Forest. The woods were eventually overgrown with giant Deku Babas. The Phantom led its spectral forces into the Forest Temple. Ganon, now again Ganondorf back in the world of light, personally went to Death Mountain and subjugated the Goron race. With his newfound powers, he resurrected an ancient dragon, Volvagia, to whom Ganondorf would feed his Goron captives.

Zora's Domain was left completely frozen, and Lake Hylia dry by placing Morpha within the Water Temple.

In this time of crisis, Princess Zelda went under the alias as Sheik, claiming herself to be the last of the ancient Sheikah ninjas.

During this time, a Gerudo rebellion led by Nabooru resisted the new rule of Ganondorf and attacked the Spirit Temple. Link, who traveled back in time using the Pedestal of Time seven years into the future, assisted in this rebellion. Ganondorf's surrogate mothers, Koume and Kotake, abducted her in response. Link traveled back to the future to quell this.

Seven years later
In these seven long years of the brutal rule of Ganondorf, Link's soul was lying dormant in the Temple of Light in the Sacred Realm. Rauru, the sage of Light, believed Link to be too young to be the Hero of Time, and had him age seven years in the temple.

Link, now awakened as the true Hero of Time at age seventeen, was to awaken the other six sages to unlock the power to overthrow Ganondorf. In the future events, Link would be assisted by Shiek. With this, Link set off and awakened Saria, his childhood friend, as the sage of the Forest Temple after besting Phantom Ganon in combat. With a combined effort between Link and Darunia, the Fire Temple was stormed, freeing the Goron slaves and slaying Volvagia with the ancient Megaton Hammer. Darunia was awakened as the sage of the Fire Temple.

Princess Ruto and Link attacked the Water Temple under Lake Hylia and destroyed Morpha, which allowed water to flow into Lake Hylia once again. Princess Ruto was awakened as the sage of the Water Temple.

Ganondorf opened the Kakariko Well, releasing the ancient beast Bongo Bongo, and leaving Kakariko in ruin. After traveling back in time and raiding the Bottom of the Well, Link penetrated the Shadow Temple and slew Bongo Bongo, awakening Impa the sage of the Shadow Temple.

Link sent himself back into the past to penetrate the Spirit Temple. After a chain of events there which resulted in the Gerudo rebel Nabooru being kidnapped by Twinrova, he traveled back to the future after altering the eviroment of the temple to allow himself in there as an adult.

Link eventually reached the chambers of Twinrova, where an Iron Knuckle stood guard. After a brief skirmish, the Knuckle was revealed to be Nabooru, under mind control. Twinrova was eventually killed, their bickering spirits ascending into the afterlife. Nabooru awakened as the sage of the Spirit Temple.

The power of these new sages opened a path into Ganon's Castle.

Finale
At the top of Ganon's Tower housed inside the Castle, Ganondorf ominously awaited, playing an eerie song on his organ. As Link reached the summit of the Tower, Ganondorf, demanding the Triforce of Courage from Link, attacked Link and incapacitated Navi, who was unable to assist Link at this point.

A massive skirmish ensued in Ganondorf's chambers, which would ultimately lead to the destruction of the castle after the alleged death of Ganondorf, impaled in the throat and vomiting blood.

Link and Zelda fled the collapsing castle, and narrowly made it out. The castle imploded onto itself following the escape of the two, leaving almost nothing left. A strange noise from the ruins of the castle caught Link's attention. Apparently, the Triforce of Power would not let Ganondorf go.

Emerging from the rubble, Ganondorf unleashed his hidden powers through the Triforce, turning himself into something much more sinister. Link, disarmed by Ganon, improvised using a combination of light arrows, Biggoron Sword, and the megaton hammer, eventually giving himself time to retrieve his Master Sword, and allowing Zelda to hold the beast down, leaving Link to impale Ganon, giving the Seven Sages time to open the void into the Dark World and flinging Ganon in.

Aftermath
Hyrule was left in ruin following the aftermath of the Imprisoning War. Hyrule Castle and Castle Town was nothing but rubble, Zora's Domain frozen over, and the various provinces still recovering from the curses. Zelda used the Song of Time to send Link back in time seven years earlier, retrieving his childhood.

Timeline split
When Zelda sent Link back to the past, she unknowingly created a massive time paradox and split the universe into two parallel timelines: the "past timeline" and the "future timeline". In the past timeline, peace reigned throughout Hyrule, with Ganondorf captured before he can take over. Link would soon travel to Termina to pacify the evil from Majora's Mask. 100 years into the timeline, Ganondorf would manipulate Zant of the Twilight Realm and conceive a massive plot to take over Hyrule.

However, all was different in the future timeline. Hyrule would be left in ruin, and in the midst of recuperating, Ganon would escape the Sacred Realm. Link, sent to the past, would not be present to save them, and the gods initiated The Great Flood to destroy Ganon and his forces, along with the rest of Hyrule. The population would escape to the mountaintops, and inhabit the newly formed Great Sea. Ganon would once again escape, as somehow the undersea seal wore off, and was set on "draining" Hyrule and claiming it. Link would be reincarnated into this timeline to slay Ganondorf.