Zelda and Link after the battle, noticed The Great Sea to be falling apart, and decided to find a new land to call home and when they moved the people they tried to make it as much like The Hyrule lost beneath the waves as possible and founded a lake, Lake Hylia a mountain, Death Mountain and the Town, Kakariko Village, and a desert named after the old one. They then moved the Master Sword to a secret Shrine making three pendents required to lift the Master Sword, and hiding them throughout Hyrule. Finally, after all these efforts they made a Castle in the center of Hyrule and called it Hyrule Castle after the old one.
After that they were forgotten and all that remained were their bloodlines. Links became very faint until only two people were left who contained it. These two were a 16 year old boy named Link and his Uncle.
Ganon escaped Hyrule only to become trapped in the Sacred Realm of the New Hyrule along with the Triforce which gave him the wish of claiming the Sacred Realm and turning it into a world of evil called the Dark World however the sages seal kept him trapped forcing him to summon an evil within Hyrule to perform his dirty work.
The person he summoned was a mage called Aghanim who captured all of the six maidens in Hyrule who were the Descendents of the seven sages this leaved only Princess Zelda to break the barrier and free Ganon from the Dark World.
Chapter 5: The Knight's of Hyrule
One night on a very stormy night Zelda telepathically called Link's descendents to help rescue her from Aghanim. Link's Uncle answered her first then Link. When Link got to the castle he witnessed his Uncle die, and received his sword and shield.
Inside the Castle Link searched high and low until he came upon a Ball and Chain Knight guarding Zelda's cell. After a tedious battle he grabbed the guard's key and led Zelda to the throne where she explained how to get into the sewers which was the only secret exit out of the castle. After hours of walking through the sewers they arrived at last at the chapel quite a ways away, where the priest promised to guard Zelda with his life.
Link went to town to come up with a plan of what he should do to became strong enough to fight Ganon. In town he was told to search for the town elder in a far away place. After searching long and hard he came upon this old man who told him to get a pendant out of the dungeon nearby to prove whether or not Link was worth his time.
Link whipped through the dungeon and came back to learn about the Master Sword guarded by three pendents one of which he had just gotten then he recieved the Pegasus Boots used by the Sages themselves, and was told to find the other two pendents to gain the Master Sword so he too could fight for Hyrule.
Link found the second one in the desert to the far west of the first one and the third to be on Death Mountain to the far north. At Death Mountain he recieved the the mirror used to warp between the worlds and the stone used to prevent from changing into a bunny when in the Dark World.
Link then traveled to the Forest to the Far North West and at last claimed the Master Sword for his own. At this same time Zelda was being once again kidnapped and Link arrived too late to save the priest or Zelda, and was told by the dieing priest to save Zelda.
Link then traveled back to the castle and found a secret tower on the roof and inside was several rooms filled with Ganon's finest monsters, but to the Master Sword they were no challenge. At the top he finally caught up to Aghanim and faught hard but before the final blow Aghanim ran through the warp to the Dark World and Link followed.
In the Dark World Link noticed the many similarities in the landscape and also the many differences between the two worlds. After his observations, Link set out to rescue Zelda and the six maidens. The first two were easy and one was in the north and the other in the south. Link then traveled west to the town of thieves which had replaced his beloved Kakariko Village. Along the way however he noticed a bomb shop sitting where his home once layed. Link then found four more maidens which like the other two were in special hand sized crystals. They all told him where Zelda was hidden and he was directed to Turtle Rock a dungeon to the East of Ganon's Tower both atop Death Mountain. Inside Link found many of the hardest traps ever seen but once again was victorious and rescued Zelda also contained in a crystal, and putting her and the six maidens together formed enough power to break the barrier on the entrance to Ganon's Tower.
Once inside Link faught heroically through the hardest dungeon in his adventure and refaught the bosses he had previously killed in the Light World, including a final battle with Aghanim. After the four battles had been faught Link witnessed Ganon turning into a bat and flying off Link summoned his bird and followed and found himself at the Pyramid of Power fighting Ganon to the death and was victorious in completely destroying Ganon. 0He then walked into a secret chamber and claimed the Triforce wishing for it to cleanse the world of all Ganon's evil deeds including the many people trapped in the Dark World and all the people killed in both worlds. The Dark world was then changed into a land formed from Link's hopes, dreams, and wishes.
Afterwords Link went back home after witnessing the king's revival, and saw his uncle waiting inside for him. The next day Link and his Uncle went to the castle, and Zelda thanked Link for all his hard work and over the years they became great friends.
Epilogue:
Link then knowing the dangers of the world began to travel away from Hyrule in search of further evil to destroy. The Master Sword was then left in its shrine to await the next chosen one.