After Ganon's defeat the seven sages began to seal Ganon into the Sacred Realm after successfully doing so, a great war called, "The Imprisoning War" Began. In this war Ganon's army faught fiercely against the soldiers inside the castle. Ganon then escaped and killed the seven sages and the two sages protecting the Master Sword. Then he formed an army which was about to destroy Hyrule. But the gods listened to the pleas for help from the Hylien's and Sealed Hyrule under a vast ocean spreading the specifically selected people across the islands jutting up from the surface.
Ganon later escaped leaving most of his power under the surface.
During this next period of years the Zora's divided in half, half became a corrupt species called Octorocks the other became a tribe called the rito which remained peaceful. The Goron's were lost and only a few remained but were never seen by Hylians. The Gerudo were intermixed with the Hylians and were forgotten. The Kokiri became a tribe called the korocks.
The Legend of Hyrule was almost completely lost to this new race of people due to their unawareness of Hyrule below the waves and to their clouded memory. After all Hyrule was sealed only 100 years before the new Link.
Chapter 3: Rise of a New Hero
The new Link was raised on an island named Outset Island, an island who honored a the Legend told by the mysterious wanderor of old and made sure to pass on the Legend from generation to generation, and when children came of age they were required to hone a tunic, a sword, and shield to represent their courage like the Hero of Time from the legend.
Link and his sister Aryll were raised by their grandma peacefully until Links 16th birthday when he came of age. Later that day a huge bird and a bunch of pirates came and Link saw the bird snatch a pirate which angered Link causing him to chase it all the way to the top of the island where a forbidden forest was located. In this forest he rescued the Woman and saw the bird kidnap Aryll instead this time, and that angered Link so much that he ran off the cliff just to foolhardedly swipe at the bird. The Woman grabbed Link before he fell off however and later offered to take him aboard her ship to try and help him.
After saying goodbye to his grandma, Link set off with the pirates to the Forsaken Fortress. He was then sent in a barrel onto the Fortress. Unforetuneatly he lost his sword. After sneaking past countless Dumbass Henchmen he came to the top where he found his sword, at the top he found his sister and two maidens, but the bird threw him far away in the sea.
When he awoke a boat called the King of Red Lions began speaking to him telling him to collect 3 stones, and a sail, Link excepted.
The first stone he found after clearing out a vile volcanoe at Dragon Roost Island which was given to him by the Rito Prince. The second stone he got after rescueing Makar from the Forsaken Forest, from the Great Deku Tree. The third stone was handed to him by the great god of the sea after he told of his plans to save his sister and Hyrule.
After setting the three stones on their alters Link entered the Tower of the Gods which had just surfaced. Within this majestic tower Link was amazed, and bewildered by what he saw inside but this did not stop him and after much toil and trouble he met a futuristic Boss and finished him. A portal then shone brightly at the foot of the tower.
The portal took Link and the king of red lions to none other than Hyrule Castle. Inside was a black and white grand castle completely trashed with hundreds of enemies with looks of pain and fear on their faces frozen completly in time.
Link found near the back a complicated puzzle but solved it without too much trouble, and then the statue of the Hero of Time moved out of the way revealed a basement. In this basement Link found a legendary sword on an alter with beutiful stain glass windows of the sages from long ago. Link then pulled the sword unaware of the consequences, and the castle was completely turned back to normal all the color was restored and time itself, however it was 100 years in the past in the great battle for Hyrule, and Link was in the middle of it. Also Ganon's powers were completely rejuevenized.
After that Link faught hard against all kinds of enemies throughout the castle until they were all gone when he was finally able to leave. Outside he showed off The Master Sword to the king of red lions, and went back to the surface.
At the surface the king of red lions told Link to rescue his sister from the Forsaken fortress once again, and after many battles he made it to the top when the pirates appeared and took Aryll and the two maidens promising to return them safely.
Link then faught bravely against the dangerous bird who had tossed him aside before, until its death. After the battle link and Tetra the leader of the Pirates kept climbing until they met up with a man who called himself Ganon. Link then overreacted and slashed at Ganon using the Master Sword and then felt sick when he learned that Ganon had killed the two sages protecting the sword's power. Ganon's Triforce of Power then began glowing and he realized that Tetra was a descendent of princess Zelda. However by this time it was too late and the dragon and the rito from Dragon roost Island flew away taking them with them to the Tower of the Gods.
Inside Link took Tetra to the alter where the Master Sword had lain and a man was standing there pulling out a piece of the Triforce of Wisdom he took Tetra's necklace and put them together then they shone brightly and became the full Triforce of Wisdom which turned Tetra into Princess Zelda. The king of Hyrule then said he was trapped in Hyrule Castle and his soul was in the king of red lions.
The king then told Zelda to stay in Hyrule Castle for her own safety, and for link to find two new sages to repower the Master Sword. The first sage turned out to be his friend from Dragon Roost Island. The second sage was none other than Makar whom he rescued from The Forsaken Forest.
After repowering the Master Sword completely the king of red lions told him to gather the eight fragments of the Triforce of Courage using Tingles chart to find the eight separate charts which used one at a time whould find the eight pieces of the Triforce of Courage which combinded would the form the final Triforce which combined with Ganon's Triforce of Power and Zelda's Triforce of Wisdom would make the complete Triforce handed down by the gods.
After doing so he descended down to Hyrule using the Triforce of Courage and broke the barrier between the Castle and Ganon's Tower. Once inside the Tower Link faught each of the four bosses he had previously killed but now in black and white. At the end he found Zelda in the hands of Ganon. He then killed puppet ganon and faught against the real Ganon and sealed him underwater when the Barrier between Hyrule and the world above dissapeared finally flooding Hyrule killing the king and ganon underwater.
Zelda and Link however escaped and were fated to rebuild hyrule.
Chapter 4: The Mysterious Ship
Link, Zelda, and her crew sail into foreign sea's while exploring, and eventually come upon a mysterious ship. Zelda boards it, and dissapears. Link soon follows, and falls over board. When he comes to, he's on an unknown island far from the Great Sea, Zelda's nowhere to be found, and neither is her ship. Link begins his adventure across new seas in order to save Zelda. After much adventuring in foreign seas Link did succeed and returned home with Tetra.
Epilogue:
After Links voyage ended and he arrived back home in Hyrule, he and Zelda witnessed the fall of the ocean over the coming years.