Time Line

This time has five Zeldas and four Links. The first Zelda is the one put to sleep by the evil wizard. After her, all the princesses are named Zelda, not just the ones with Roman numerals after their names. I refer to the Zelda in OoT and LoZ/AoL as Zelda I, the one in TWW as Zelda II, the one in ALttP as Zelda III, and the one in the Oracle games as Zelda IV. The sleeping Zelda in AoL is, of course, the original Princess Zelda. Note that, in TWW, I use the names "Ganondorf" and "Ganon" interchangeably.

The history of Hyrule, according to this theory, is as follows:

Key
      - Link I and Zelda I (OoT, MM, LoZ, AoL)
      - Alternate Future (second half of OoT)
      - Link II and Zelda II (TWW)
      - Link III and Zelda III (ALttP, LA)
      - Link IV and Zelda IV (Oracle, LA)

Date Event Source
0 H.R. According to legend, the golden goddesses Din, Nayru and Farore create the world of Hyrule and all the life forms in it. Before departing for the heavens, they leave behind their gift to the world: the Triforce, three golden triangles that can grant their holder's greatest wish. A Golden Land begins to flourish around the Triforce's hiding-place, and the Triforce beckons to people from the outside world, in hopes of finding somebody worthy of its power. OoT and ALttP manuals
1000 H.R. The Hylia, the chosen people of the goddesses, settle in various parts of the world, passing on their knowledge and magical lore to many people. Around this time, the kingdom of Hyrule is founded in the small land south of Death Mountain. The Triforce is possibly used by these ancient people. ALttP
2099 H.R. A great Hylian king, who has used the Triforce to keep the peace and unite the different races of Hyrule, dies, and his son inherits part of the Triforce. An evil wizard, working with the prince, puts the prince's younger sister, Princess Zelda, to sleep for refusing to give information about the Triforce and then dies. The prince decrees that every princess in the royal line shall be named Zelda so this tragedy will not be forgotten. AoL manual
3000 H.R. Great sages, including Rauru, the Sage of Light, realize that the Triforce poses a hazard if it falls into the wrong hands. They put the Triforce back in its resting place in the Golden Land and build the Temple of Light to house it. The Temple of Time, along with the Master Sword, are built to guard the entrance to the Sacred Realm. OoT
4000 H.R. The Book of Mudora, compiling all the legends and myths in Hyrule, is compiled. ALttP
5000 H.R. By now, not even the Sages know where the Triforce is hidden. Lust for the Triforce's power is strong, and the people of Hyrule, suspicious that one group or another is hiding the Triforce, attack each other. Hyrule is engulfed by a fierce civil war. OoT, ALttP manual
5040 H.R. Link I and Zelda I are born in Hyrule. To escape the fires of the war, Link's mother takes him to the forbidden forest. There, the Great Deku Tree takes him in, and he is raised a Kokiri. OoT
5050 H.R. The King of Hyrule stops the fighting, and a time of peace takes effect as the King attempts to unite Hyrule. Ganondorf, the King of the Gerudo thieves, secretly continues to search for the Triforce. OoT
5051 H.R. Link I, now a young lad, leaves the Kokiri Forest on a quest to stop Ganondorf's plot to enter the Sacred Realm. Link opens the entrance to the Sacred Realm by drawing the Master Sword, but his spirit is sealed away for seven years until he is old enough to be the Hero of Time. Meanwhile, Ganondorf and his band of thieves enter the Sacred Realm. Ganondorf gets the Triforce of Power, and uses it to become the Evil King Ganon. The Triforce of Wisdom goes to Princess Zelda, and the Triforce of Courage goes to Link. As Ganon builds his power, Hyrule is consumed by darkness. First half of OoT
5051 H.R. Link I wakes up, having battled Ganon in the alternate future, and warns Zelda I about Ganon's intentions. He doesn't realize that the Triforce of Courage is still hidden in his heart. OoT
ending
5051-
5057 H.R.
While Link sleeps, Ganon takes the opportunity to conquer Hyrule and set himself up as the Evil King of Hyrule. Seven years later, Link I returns as the Hero of Time. Freeing the Sages, he defeats Ganondorf. Ganondorf transforms into Ganon, but Link holds Ganon off long enough for the Sages to seal him in the Sacred Realm. Zelda I sends Link back in time, ending this alternate future. Second
half
of OoT
5051 H.R. Link departs to find a valued friend, and finds adventure in the parallel world of Termina. While he is away, Zelda splits the Triforce of Wisdom, and Ganon kidnaps her. Link returns to Hyrule and saves Impa, who tells him about their plight. Link recovers the Triforce of Wisdom, reduces Ganon to ashes, recovers the Triforce of Power, and saves Zelda. Majora's Mask, LoZ
5056 H.R. Link approaches the age of 16, and one day the Triforce symbol appears on his hand. Going to see Impa about it, she tells him about the ancient Princess Zelda, who is still under the sleeping spell. In the Great Palace Link discovers that the Triforce of Courage has been hidden in his heart all along, and with the united Triforce he awakens the first Princess Zelda from her ancient sleeping spell. AoL
5058 H.R. Link leaves Hyrule, and the Triforce of Courage leaves his body and shatters into eight shards, which come to be hidden around Hyrule. With Link gone, Ganon's followers use this opportunity to revive Ganondorf. The Triforce of Power falls into his hands, and from his hiding place in the tainted Sacred Realm, Ganon covers Hyrule with darkness. The King of Hyrule orders the Sacred Realm sealed, but Ganon's army attacks the castle. As the Knights defend the Sages from Ganon's monsters, the Seven Sages seal Ganon inside the Golden Land. This battle comes to be known as the Imprisoning War in later centuries. ALttP, TWW
5300 H.R. Ganon's power is returned to him, and he kills the descendants of the seven sages, allowing him to escape from the Dark World back into Hyrule. He covers Hyrule with darkness, and kills the sages who were giving the Master Sword its power. Ganon builds a tower and an army in preparation to take over Hyrule. The people wait for the Hero of Time to return, but he never does. TWW
5302 H.R. Ganon's army attacks Hyrule Castle. In their last desperate hour, the people of Hyrule pray to the gods. The gods decide to bury Hyrule under torrential rains. The people of Hyrule are ordered to take refuge on mountaintops. The Master Sword forms a seal freezing Hyrule in time, and keeping Ganon's power sealed away. Hyrule is buried at the bottom of the ocean, and life begins anew on islands formed from Hyrule's mountaintops. A piece of the Triforce of Wisdom is given to the descendants of the Royal Family, and they are charged with guarding it. The King remains below, waiting for a day when Hyrule can be revived, charged with finding a hero in case Ganon is revived. TWW
5590 H.R. On Outset Island, Link II, a boy unrelated to the Hero of Time, is born. A girl is born to a great female pirate captain, and is named Tetra. TWW
5601 H.R. Ganon is revived once again, and is able to make a portal leading to the surface world. Taking over the Forsaken Fortress, he sends his servants over the ocean in search of the missing pieces of the Triforce. TWW
5602 H.R. Link II celebrates his coming-of-age, but his younger sister Aryll is kidnapped by one of Ganondorf's servants, confusing her for Tetra. Asking for help from Tetra's pirates, Link tries to invade the Forsaken Fortress, but is thrown from the tower. A mysterious boat rescues him, and leads him on a quest to get the Master Sword, the only blade that can defeat Ganon. After collecting three pearls, and passing the test of the gods, a portal appears, leading to the frozen world of Hyrule beneath the waves. Link takes the Master Sword from Hyrule Castle, but this releases the seal, unfreezing Hyrule and releasing Ganon's full power. Link saves his sister with the help of the pirates, but the Master Sword has no effect on Ganondorf. Tetra, the young female captain of the pirates, and Link are rescued and taken to Hyrule. There, the King of Hyrule reveals that Tetra is actually Princess Zelda, and gives her the rest of the Triforce of Wisdom. The King was the guiding force behind the boat. He leads Link on a quest to return the power of evil's bane to the Master Sword, and to find the hidden Triforce of Courage shards. Armed with these weapons, Link arrives back in Hyrule to discover that Zelda has been kidnapped. Breaking Ganon's barrier around Hyrule Castle, he climbs Ganon's Tower. At the top, Ganondorf is able to steal the other two pieces of the Triforce from Link and Zelda. But before he can touch the united Triforce, the King touches it and wishes for Hyrule to be buried under the waves for good. Link and Zelda defeat Ganondorf, turning him to stone when Link sticks the Master Sword in his head. But Hyrule is buried under water, and Link and Tetra must now find a new land to call Hyrule. TWW
5603 H.R. A new Hyrule is founded. -
6000 H.R. Link III and Zelda III are born in Hyrule. -
6014 H.R. Many disasters suddenly plague Hyrule. ALttP manual
6015 H.R. Agahnim appears in Hyrule, stops the disasters, and is made one of the King's top advisors. He secretly overthrows the King, and begins sending the descendants of the Sages into the Dark World, in a plot to free Ganon. Zelda III contacts Link III, the Legendary Hero, telepathically. Link II fights Agahnim, but Agahnim is able to break the Seven Sages' Seal. Link goes on to save all of the maidens from the Dark World. He completely destroys Ganon, and claims the united Triforce. Link uses the Triforce to do much good. ALttP
6015 H.R. The people of Hyrule fear what evils may arise from Ganon's ashes. Ever diligent, Link III leaves on a journey of enlightenment. Link's Awakening
6016 Link's journey now complete, he begins sailing back to Hyrule. However, a sudden squall destroys his ship, and Link drifts to the island of Koholint. There he defeats Nightmares to gather together eight Instruments and wake the Wind Fish. Koholint Island disappears, and Link is left once again with the flotsam of his ship. He drifts, possibly back to Hyrule. Link's Awakening
6100 H.R. The united Triforce is placed in Hyrule Castle. As it rests, it watches over Hyrule. Inferred from OS
6493 H.R. Link IV and Zelda IV are born in Hyrule. -
6500 H.R. Twinrova masterminds a plot to revive Ganon. By sending Onox to Holodrum and Veran to Labrynna, she plans to light the three flames of Sorrow, Destruction, and Despair. This would bring Ganon's spirit back from the beyond, and then Princess Zelda's body would be used to revive Ganon. Oracle
6505 H.R. The Triforce sends Link IV on a mission to Holodrum. There, Link is able to defeat Onox, saving Din, the Oracle of Seasons, but nonetheless the Flame of Destruction is lit. OoS
6507 H.R. The Triforce sends Link IV on a quest to Labrynna. Link prevents Veran from destroying Labrynna, but cannot prevent the Flames of Sorrow and Despair from being lit. Princess Zelda travels alone to Labrynna to help Link. Twinrova kidnaps her, planning to use her pure body to revive Ganon. Link rescues Zelda by defeating Twinrova, but Twinrova sacrifices herself to revive the Evil King. Link defeats Ganon, banishing him from the world. OoA