The Official TimelineEdit
| Spoiler warning!|
This article contains plot details.
It starts out with Skyward Sword. Link banishes the evil on the surface, just as it's mentioned in the beginning of The Minish Cap, which is next in the timeline. Vaati is born after Skyward Sword and causes trouble after Hyrul Kingdom is established. He then comes back in the next game, Four Swords. Vaati is now defeated. The Hyrulean Civil War starts. Link is taken to Kokiri by his dying mother.
Ocarina of Time is the game that makes the series split into three endings. It either ends with Link failing to defeat Ganon, Link defeating Ganon and going back to a child, or Link defeating Ganon and staying as an adult. We will call the first one story A, the second one story B, and the last one story C. The Great Sealing War, also known as the Imprisoning War, takes place during Ocarina of Time. It has the Sacred Realm being opened, the Triforce being scattered, the Sacred Realm being transformed into the Dark World, and Ganon being put into the Dark World by the Sages.
After the Sealing War, A Link to the Past takes place and Has the death of Ganon. Unfortunately Ganon is revived in the Oracle games which come next. After that, Link is washed up onto the island of the Wind Fish where he frees all of the people in Link's Awakening. The Triforce is later used for monarchy, which results in Ganon stealing Zelda for her Triforce of Wisdom in The Legend of Zelda. Link saves her and kills Ganon for good. Link has to go on a quest several years later to free Zelda from a deep sleep in The Adventure of Link. Ganon's minions are after him because they can revive Ganon if they get his blood. Link saves Zelda and defeats the forces of Ganon to prevent Ganon's revival. Thus Hyrule is saved!
This is the ending of Ocarina of Time that we all see when we beat it. Link goes back to a kid and the Door of Time is sealed. Navi left right before the door was sealed though. Link went to the forest to look for her and started the story of Majora's Mask. After that, he got older, had kids, and died. Twilight Princess comes next after Ganondorf is revived by Zant. Apparently Ganondorf didn't die at the end of Twilight Princess because he used a Trident from the Gerudo to turn into Ganon in Four Swords Adventures. Because of Ganon's deeds, Vaati came back as well, causing our hero a lot of trouble. Ganon is defeated and Vaati is sealed away. Thus Hyrule is saved!
Link defeated Ganon, but he remained as an adult and allowed time to flow properly. This somehow created the Great Flood. A likely reason is Link did something to cause it that he couldn't have done as a kid. He probably didn't end up doing it in story B because he probably did someting else like have kids. Anyway, Wind Waker happens and Ganondorf is killed. After that, Link goes to the alternate world and saves Zelda and Linebeck in Phantom Hourglass. Finally, a new continent is discovered for Spirit Tracks to take place in. Demons are defeated and evil is banished. Thus Hyrule is saved!