After the events of Four Swords Adventures, a fierce civil war breaks out. The end result was a unified Hyrule, but the Gerudo were no longer on good terms with outsiders. Their new leader, Ganondorf, pledged allegiance to the new king of Hyrule, but ultimately wanted the power of the Triforce. This Ganondorf, unlike the Ganondorf in Four Swords Adventures, doesn’t break Gerudo law, and is trusted by the members of his tribe. This marks the beginning of the events of Ocarina of Time.
During the events of Ocarina of Time, Ganondorf kills six of the seven ancient sages, leaving Rauru as the only ancient sage left. Ganondorf takes the Triforce of Power, and Link and Zelda get the Triforce pieces of Courage and Wisdom respectively. Link then awakens six new sages to replace the six that Ganondorf killed. In the end, the seven sages and Link defeat Ganondorf and seal him away in the Sacred Realm. Princess Zelda feels sorry for dragging Link into the events of Ocarina of Time, so she sends him back seven years to relive his childhood. Sending Link back in time causes his piece of the Triforce, the Triforce of Courage, to shatter into multiple pieces and become scattered across the land.
This action causes a split in the timeline, and leaves the future with seven new sages, Ganondorf sealed in the Sacred Realm, and no Hero of Time. Right now I’m going to focus on the events in the future.
After years of being sealed in the Sacred Realm, Ganondorf breaks his seal and terrorizes Hyrule. Since Princess Zelda sent Link back in time to relive his childhood, there isn’t a hero to save Hyrule from Ganondorf. Due to this, the Goddesses freeze Hyrule in time, put a bubble over it, and flood the land, hoping to seal Ganondorf away under an ocean. Because of the flood, Hylians start to become an extremely rare race to find. Also, due to the Goddesses not wanting anyone to find Hyrule, they force the Zoras to evolve into the Rito. Many years after the flood occurs, the events of The Wind Waker take place.
Ganondorf manages to reach the surface of the ocean, and searches for Princess Zelda in order to get the full Triforce. The Helmaroc King mistakes a new Link’s sister, Aryll, for Princess Zelda and kidnaps her. This new Link sets out with a girl named Tetra to the Forsaken Fortress to rescue Aryll. When he fails to rescue her, he meets the King of Red Lions, a talking boat who guides Link on his journey. The King of Red Lions tells Link that he needs the Master Sword in order to rescue Aryll, and to get the Master Sword, he has to retrieve three pearls.
Link gets the three pearls and goes underwater to the old ruins of Hyrule in order to retrieve the Master Sword. When he gets it, the King of Red Lions is shocked to discover that the sword has lost its ability to repel evil. He calls a meeting with the Rito, and decides to take Link and Tetra down to the old ruins of Hyrule. There, he reveals Tetra is actually Princess Zelda, and that she should remain in the ruins to be kept safe. He also reveals that he’s an old king of Hyrule from an age before the flood. Link then must go to temples to make the Master Sword regain its abilities.
Once at the temples, it’s revealed that Ganondorf killed Laruto and Fado, two sages who kept the Master Sword’s ability intact, and that Link must replace them. When replaced, the Master Sword regains its ability to repel evil, and Link collects the shattered pieces of the Triforce of Courage. In the end, Link and Zelda kill Ganondorf, and the King wishes on the Triforce that old Hyrule is erased. He then tells Link and Tetra to form their kingdom, and not to recreate Hyrule.
Link and Tetra then set off to find a new land to form a new kingdom. A couple months after The Wind Waker, Link and Tetra run into the Ghost Ship, which teleports them to another location in the ocean. Phantom Hourglass then occurs, and Bellum kidnaps Tetra in order to take her Life Force. In the end, Link rescues Tetra with the help of Ciela, Linebeck, and Oshus. Oshus then sends Link and Tetra back to their shipmates, and the two continue on their search for a new land.
The two eventually find a new land, and they create New Hyrule. It’s revealed that this land used to be ruled by an ancient demon named Malladus, and after years of ruling, the Spirits of Good waged war against him. After a long and tiring battle, the Spirits of Good eventually sealed Malladus away under the Earth, and put down chains across the land to prevent him from escaping. They also placed the Tower of Spirits in the center of all the chains, now called Spirit Tracks, and used it as a lock. One hundred or so years pass after Link and Tetra discover this new land, and Spirit Tracks starts.
Link goes to Hyrule Castle in order to become a royal engineer, but during the ceremony, Princess Zelda slips him a note telling him to meet her after the ceremony ends. She tells Link she’s worried about the Spirit Tracks, and wants to go to the Tower of Spirits in order to make sure they’re safe. On the way to the Tower of Spirits, they’re attacked by Zelda’s chancellor, a man named Cole. He kills Zelda and steals her body in order to release Malladus from his seal. Zelda’s spirit, however, sticks around and travels with Link. In the end, Zelda and Link kill Cole and Malladus, and retrieve her body back.
Part 3 coming soon.