At the end of the Ocarina of Time, Link defeats Ganon, and Zelda and the six awakened sages seal him inside the Sacred Realm. Zelda then sends Link back in time with the Ocarina of Time, removing him from this timeline.
Some time afterward, Hyrule Castle is rebuilt and monuments to the Hero of Time and the six sages are built inside. Furthermore, the Master Sword is moved to a pedestal within the castle itself.
But eventually, Ganondorf breaks free from his seal and attacks Hyrule with the might of the Triforce of Power. This time, no hero comes to save the day, and the people pray to the gods for help. The gods decide to flood the land and seal Hyrule Castle beneath the surface. Ganondorf is stopped for now, and the races of Hyrule survive on the mountaintops which are now islands.
The events of Ocarina of Time have become legend by the time this game begins. Ganondorf survived the flood and is looking for the keeper of the Triforce of Wisdom. Link restores the Master Sword and uses it to kill Ganondorf.
The Phantom Hourglass relates an adventure that Link and Tetra have in the space of ten minutes after they have set sail to found a new Hyrule.
Set a century after the events of Phantom Hourglass, Link and Tetra had found a new land and named it Hyrule as well. A dark being, Malladus, had been sealed under the land, which Link needs to seal once more.
