Here's a nice timeline theroy written by TSA:
Click here to view the secret text
×Young Link Timeline:
AoL Backstory -> The Legend of Zelda -> The Adventure of Link -> Oracle of Seasons/Ages -> Temple of Time Constructed -> The Minish Cap -> The Imprisoning War -> Ocarina of Time (Young Link) -> Majora's Mask -> Twilight Princess -> Four Swords Adventures -> A Link to the Past -> Link's Awakening
Adult Link Timeline:
AoL Backstory -> The Legend of Zelda -> The Adventure of Link -> Oracle of Seasons/Ages -> Temple of Time Constructed -> The Minish Cap -> The Imprisoning War -> Ocarina of Time (Adult Link) -> Flooding of Hyrule -> The Wind Waker -> Phantom Hourglass
Explanation:
Creation of Hyrule.
In the beginning, Hyrule was created by the three goddesses, as according to several of the games. Din, Nayru and Farore create Hyrule and left the Triforce behind. Triforce left in the Sacred Realm. Eventually, as life comes ot Hyrule, the Royal Family of Hyrule became guardians of these secrets about the Triforce and the Sacred Realm. At this time, races of Hyrule are scattered, and the ancient Sages reside in Hyrule as protectors. Sentient beings such as Great Deku Tree, Jabu-Jabu and Valoo also are diety-like figures who protect the lands. The Minish also exist, and they begin forging gifts and weapons for the people of Hyrule.
AoL Backstory:
At some point, a Prince comes to power and wishes to have the entire Triforce. He learns Zelda was told the secrets of the Triforce on the King's deathbed, and demands her to reveal them. She refuses, and the Prince has his Wizard try to wrestle the secrets. When he fails, he casts a sleeping spell on Zelda. Artwork depicts the Prince's shadow as the "wizard"...something I've thought was interesting. I believe the Triforce was still in the Sacred Realm, and perhaps the Prince went there and tried to claim it. He only obtained power, and came back to Zelda to learn of the other two fragments. Thus, when she didn't speak and was put under a spell, the prince realized his mistakes and ordered every female born royal member to be named Zelda. I do have this theory, though, that the wizard was Ganon, and he found the Triforce of Power in the Sacred Realm (one of those interlopers). He used his power to control the prince...and when he failed, he fled. Just my theory. After placing Zelda into the North Castle, the Prince hid the Triforce of Courage, which I believe he was given after demonstrating his remorse and ability to accept responsibility, in the Great Palace. A "curse" is placed on Hyrule - that the one worthy of this piece would bear a symbol on the back of their hand
The Legend of Zelda:
Of course, Hyrule was vast and wide by this time, but one day the wizard, Ganon, returned to Hyrule to claim the rest of the Triforce when he learned the new Princess, Zelda, had the Triforce of Wisdom. He conquered Hyrule and kidnapped Zelda, but not before she was able to hide the Triforce of Wisdom in 8 fragments and dispatched Impa to find a hero. Meanwhile, Ganon fled to Death Mountain and awaited this hero. Impa found Link, a hero, and he recovered the eight fragments and unified the Triforce of Wisdom. He went to Death Mountain, defeated Ganon, and saved Zelda and Hyrule. The Triforce of Wisdom and Courage were back in Hyrule's royal family's possession.
The Adventure of Link:
Many seasons later, Link notices a strange mark on the back of his hand. He confronts Impa, and she reveals it is the mark of the "curse" - that he is destined to retrieve the Triforce of Courage. She also reveals that there is the original Princess Zelda who slumbers now as part of a terrible curse. Link sets off to find the Triforce of Courage so he can re-unite the Triforce and use it to break the sleeping spell on Princess Zelda. Meanwhile, Ganon's minions learn they can revive their master by sprinkling the blood of Link on his ashes. In the end, Link returns six crystals to their palaces to break the seal on the Great Palace, and then recovers the Triforce of Courage. The Triforce is reunited in Hyrule, and Hyrule is at peace.
Oracle of Ages/Seasons:
I do not know if this is the same Link, but I would assume it is. You can argue that Link and Zelda don't know each other because the Zelda he saved didn't really get to know him (despite the behind-the-curtain moment in Zelda II). Link is studying the Triforce in Hyrule Castle when he is sent to far off lands that are under attack. Link has to save Holodrum and Labrynna from the evil of General Onox and the Sorceress Veran (don't they both look like Twili beings?), before finally realizing Koume and Kotake, two Gerudo Witches, were trying to revive Ganon through Zelda. Link defeats them and the shell of Ganon, and saves the two worlds and Hyrule once again.
The Minish Cap:
Much time passes, and the Kingdom of Hyrule is at peace. There is a tournament held in Hyrule to honor swordfighters, who get a chance to be in the presence of an ancient blade given to the Hylians by the Picori (The Minish). It seems that one of the Minish, named Vaati, got wind of a magical power known as the Light Force, which he became obsessed with. He stole his master Ezlo's magical cap and used it to become a human. He also used it to turn Ezlo into a talking hat. Vaati goes to Hyrule and believes the Light Force is sealed in the chest the ancient Picori Sword is used to seal. But when he opens it, he finds there is nothing inside, and in his rage turns Princess Zelda to stone. Link, who had accompanied her during the day, tried to stop Vaati but failed. In order to stop Vaati and save Zelda, Link needs to repair the Picori Sword and is sent to find The Minish. He finds Ezlo, who reveals how he can travel between the Minish world and his own, and how to repair the sword. After collecting the four elemental stones, Link reforges the Picori Sword into the Four Sword, and uses it to slay Vaati and save Zelda. Ezlo then returns to his world. The Four Sword is used as a seal on Vaati.
The Imprisoning War:
Word gets around Hyrule of the Sacred Realm and the Triforce, and people begin to go searching for it. A fierce war breaks out between the Hylians and those who went to the Sacred Realm searching for the Triforce. Evil spills forth into Hyrule, and the King of Hyrule orders the sages to seal the entrance to the Sacred Realm. They erect the Temple of Time as a gateway to the Sacred Realm, and forge The Master Sword as a safeguard on the gateway. The Blade of Evil's bane is a sword that evil ones can never touch, and is the final protection to the entrance to the Sacred Realm. In addition, three Spiritual Stones are used as keys to opening the "Door of Time", a barrier to the Master Sword's chamber and the Pedestal of Time (the gateway to the Sacred Realm). The Ocarina of Time is also created. Also, those who remained in the Sacred Realm and tried to establish dominion over it were sealed away in the "Twilight Realm" by the light spirits sent back to Hyrule by the Three Goddesses. These beings become The Twili. They leave the Mirror of Twilight in possession of the ancient Sages and the Hylian Royal Family as a means to seal others away.
Ocarina of Time:
Koume and Kotake raise a new Gerudo Male, Ganondorf to become an evil king. They have him try to discover the way back into the Sacred Realm, and he does so, but realizes he can't do it himself. So, in a huge ploy, he attacks Hyrule and forces Link, a young Hylian raised by the Kokirir, to embark on a quest to find the Master Sword to open the path to the Sacred Realm so he and Zelda can get the Triforce before Ganondorf. Still, after successfully doing so, he is too young to be the "Hero of Time", choosen by the Master Sword, and is sealed away in the Sacred Realm until he ages seven years. During that time, Ganondorf made his way into the Sacred Realm and tried to claim the Triforce, but only obtained the Triforce of Power. Courage went to Link, and Wisdom to Zelda. When Link was returned, he had to reawaken the ancient sages in order to use their power to seal away Ganondorf. In the end, Zelda and Link stop Ganondorf, and her and the Seven Sages use their power (perhaps the Mirror of Twilight) to send Ganondorf to the Evil Realm (I don't think this is the Sacred Realm, but the actual Twilight Realm).
However, in the end, Link is sent back in time to his youth. He returns the Master Sword, which seals the road between times. There are now two timelines.
- Young Link Timeline -
Majora's Mask:
Shortly after Link returns to Hyrule as a youth, he departs to search for his beloved friend, Navi. On his search, he is ambushed by the Skull Kid and his fairy companions Tatl and Tael. They lead Link into the realm of Termina, which has three days until a moon will destroy it. Link learns that in order to stop this, he will need to use the Ocarina of Time to travel back in time three days over and over to relive the events. He eventually discovers he needs the aid of four Giants to hold of the power of Majora's Mask, an evil mask that took hold of Skull Kid when he stole it from the Happy Mask Salesman, and destroys the mask and the moon in the end. Link returns back to the Kokiri Forest at the end, still not having found Navi.
The Return of Ganon:
It appears that Ganondorf was not sealed away during Young Link's time, but was instead warned of by Link and Zelda. The ancient sages, who did not need to be rewawakened and took their true form, captured Ganondorf and tried to kill him. However, by some divine trick, he had the Triforce of Power still (Link had Courage and Zelda had Wisdom in Young Link's ending). They fail in slaying him, and one of the Sages is killed. So, the remaining sages seal Ganondorf in the Twilight Realm.
Twilight Princess:
About 100 years after the events of Majora's Mask, it seems Ganondorf found his way to Zant in the Twilight Realm after he was bypassed for the ruler of the Twilight Realm. Zant gains immense power, and performs a coup on the royal family. He curses Midna and then finds a way to break into Hyrule and fragments the Mirror of Twilight into four shards. Hyrule begins to fall under the power of Zant, as he forces Princess Zelda to surrender her kingdom. Link, a ranch hand in a village to the south of Hyrule, is drawn into the adventure and is befriended by Midna. The two team up to stop Zant by first trying to obtain a cursed, ancient power that the Twili once used. When this fails to stop Zant, Midna decides to confront Zant in the Twilight Realm where he is vulnerable. They seek out the Mirror of Twilight fragments, and eventually reform it and defeat Zant. But they then learn that Zant got his power from Ganondorf, and that Ganondorf is free in Hyrule. Link and Midna return and confront the Evil King. In the end, Ganondorf is slain by the Master Sword and he loses the Triforce of Power. Midna returns to her normal form and returns to the Twilight Realm, and shatters the Mirror of Twilight. What happens next is not known.
Unknown Adventure:
An adventure has to happen explaining what happened to Ganon and the Triforce, hopefully.
Four Swords/Four Swords Adventures:
A new Ganondorf stumbles upon the ancient weapon which holds great evil (Trident, which is much like the one Midna used with the mask) and the Dark Mirror - maybe the Mirror of Twilight? He uses it to enter the "Dark World" (a shadow world of Hyrule) and kidnaps Zelda and imprisons seven maidens who are the descendants of the ancient sages. Link is drawn to Zelda as she is capture by Dark Link, and draws the Four Sword from its seal on Vaati. This releases Vaati, whom Ganondorf then controls as a pawn to capture the maidens, whom he imprisoned. Slowly, darkness and shadow are crawling over Hyrule, and Link makes his way split into four Links to stop Vaati. He eventually does and learns Ganon was behind it all. Link and Zelda, and the Maidens, seal Ganon away in the Sacred Realm end using The Master Sword.
A Link to the Past:
Time passes, and the legend of The Imprisoning War and the Hero of Time are myths. Until one day, terrible plagues befall Hyrule, and a wizard appears. This wizard, named Agahnim, is actually a pawn of Ganon who is sealed away. Agahnim again tries to kidnap seven maidens to break the seal on Ganon, who was imprisoned in the Sacred Realm, which became the Dark World. Link is called by Zelda to save her, and then sets off to recover the Master Sword, which was laid to rest at the end of Twilight Princess, to stop Agahnim. But he is too late, and the seal is broken. The only way for Link to save Hyrule now is to confront Ganon in the Dark World and defeat him. Link rescues the maidens, who break the barrier to Ganon's Tower, and Link slays both Agahnim and Ganon, en route to claiming the Triforce. Link uses the Triforce to rid the Sacred Realm of evil, and returns peace to the land. Link then departs Hyrule.
Link's Awakening:
After many adventures away from Hyrule after ALttP, Link decides to return to Hyrule. However, he is shipwrecked and lands on Koholint Island. He soon discovers the only way to leave the island is the wake the Windfish atop the highest mountain by collecting the eight Siren's Instruments. When Link finally does so, he learns the island was all a dream, although the Wind Fish exists afterwards. Link floats away in the end, presumably back to safety, but what happens after is unknown.
- Adult Link Timeline -
The Great Flood:
After Link went back in time, Ganondorf was sealed away and Hyrule was at peace in the future Link left. But sometime after Link departed, Ganondorf broke free with the Triforce of Power, and nobody could stop him, and no hero arose. So the people prayed to the gods, and they had a select choosen few flea to safety before flooding Hyrule. Many centuries passed.
The Wind Waker:
Ganondorf escapes his ocean prison, and begins seeking the Triforce pieces. Eventually he captures Link's sister on Outset Island after trying to capture a pirate girl named Tetra, and Link and Tetra set off to save Link's sister. Along the way, Link is tossed to see after confronting Ganondorf, and is rescued by the King of Red Lions. The talking boat explains to Link he needs to find The Master Sword, and they set off to recover the three goddess pearls. When they do, the open the Tower of the Gods, which opens the path to Hyrule below the ocean. Under the waves, Link goes to Hyrule Castle and recovers the Master Sword. But when the two return to Ganondorf's fortress, the blade is useless. It is then discovered Ganondorf killed the sages responsible for the power behind The Master Sword, and Link must find new sages to replace them. Also, during this time, it is discovered Tetra is actually Princess Zelda, who possesses the Triforce of Wisdom. The King of Red Lions is also an ancient King of Hyrule who is trying to stop Ganondorf. The king and Link leave Zelda in Hyrule Castle, and then has Link go to awaken the sages and they return the power to the Master Sword. However, in order to return below the ocean, Link must prove his worth and has to claim the eight fragments of the Triforce of Courage that were hidden throughout Hyrule after the Hero of Time left. Link reunites the pieces, and goes back to Hyrule only to find Ganondorf beat them to Zelda, and awaits Link on top of his tower. Atop the tower, Link is defeated by Ganondorf, and he reunites the Triforce. But before he can make his wish for Hyrule, the King of Hyrule appears and touches the Triforce first. He wishes for the gods to totally destroy Hyrule and to give the children, Link and Zelda, hope. Hyrule begins to flood, and Link and Zelda defeat Ganondorf by stabbing him in the head with the Master Sword. They two then return to the surface, leaving Ganondorf, the King and the Master Sword to drown with Hyrule. The two then set off across the ocean searching for new lands.
Phantom Hourglass:
Not known yet, but supposedly takes place on The Great Sea after The Wind Waker.