After a short while after Links disappearance, Twinrova one of Ganon's servants from long ago began to make an alter to revive Ganon in. On this altar she placed three candles of Sorrow, Destruction, and Despair. She then sent two powerful women to capture the Oracles of Ages and Seasons.
After sensing the danger the power of the Triforce summoned a new Link to save the Oracles and to stop Ganons revival.
Chapter 6: The Disturbance of Seasons
Link was first sent to Holodrum to save Din the Oracle of Seasons. When Link arrived he found the Oracle in a band of performers and she showed off her special dance but soon after she was taken away and most of the band killed off. One of the members did survive and her name was Impa Zelda's nursemaid and she explained to Link that she is Zelda's nursemaid but was ordered by Zelda to escort the Oracle of Seasons to the castle.
Link then explored a nearby cave and gets the wooden Hero Sword. In the nearby town Link talks to the Maku Tree to get the key to the first dungeon and advice on what to do next.
After traveling to the first dungeon he beat the boss inside and later got the rod of seasons and the boomerang. Using these he eventually beat the other seven dungeons, and appears before Onox to finish her off once and for all.
After an exciting battle Link killed Onox and saved Din. Although Link faught long and hard he was unsuccessful in preventing Twinrova from lighting the candle of Destruction.
After the bad news the Triforce beckoned Link to Save Nayru and he did just that.
Chapter 7: The Disturbance of Ages
Link then traveled to Labrynna on a mission to save Nayru. Once he arrived he met up with Impa once again and recieved the hero's sword again after he broke the spell cast on her.
She led him to town and he met up with the Maku Tree learning of the changes caused by Veran's evil.
He then traveled through time to the past and visited the town learning as he went of the changes due to evil. Later he found the first level beating it without difficulty and recieved the magic harp soon after which granted him the full power to warp through time. He also beat the other seven levels and learned the horrifying truth that while he had been exploring dungeons Zelda had come to help him and got captured by Twinrova and the candles of Sorrow and despair from being lit. Link however catches up with Veran and defeats her saving the Oracle of Seasons and goes on to defeat Twinrova also but Twinrova suspected this and before the final blow sacrificied herself to complete the ritual to revive Ganon from the beyond. After so he had a final show down with Ganon and killed him, as well as Twinrova.
Chapter 8: The Terrible Storm
After saving the two oracles, Link felt satisfied with his accomplishments, and began to sail back to Hyrule, but got caught in a heavy storm, and was lost at sea. He later woke up to find his ship lost at sea, his sword gone, and his shield lying at the far corner of the house he was in.
The residents of the house and of the island began to explain of their discovery of him and his shield and told him to go to the beach and search the reckage of his raft to collect anything else that might have been spared from the sea he then found his sword lying on some broken wood left over from his raft.
An ancient owl who was the guardian of the Wind Fish then came before Link and told Link of the misfortune befallen upon them for they were stuck in a nightmare of the Wind Fish a dream not easily escapable, and that the only way to escape was to play eight instruments in front of the Wind Fish, and these wouldn't be easy to find but Link was determined to find them and began looking.
He found the first instrument in a cave near the beach and another in the mountains, the third in a cave in the canyon river, the fourth near the river, fifth at the mermaids lake, and found the sixth one in the Face dungeon, the seventh one on an eagles lookout and the eight one in the mountain tops. After he found the eight one he traveled to the Wind Fishes Egg at the top most part of the mountain to the north. He then faught caotically fighting many Nightmares. Until finally the Wind Fish woke up causing the Island to dissapear the WindFish to become a whale, the residents to become seagulls, and Link to appear on his broken sail drifting.
Epilogue:
While Link was gone, Zelda, and the two oracles went home to Hyrule. The king at that time took the Triforce of Courage and hide it in a secret dungeon far away. The greedy prince and an evil wizard later asked Zelda where the Triforce of Courage was hidden so he could claim the whole Triforce for himself, but Zelda refused and was put to sleep by the wizard. The wizard soon died keeping her secrets hidden within her waiting to be released when the hero awakens her.