It had been only thirty years since Link had come back to Hyrule from his adventure in Termina and he had already raised his first son Edgar until the boy was fifteen. After he had returned, Link helped Zelda convince her father of Ganondorf's treachery. After they succeeded in capturing Ganondorf, the King put him into the dungeon. Link and Zelda started to develop a romantic relationship shortly afterwards.
As it turns out Zelda had an older brother who was next in line for the throne, but her older brother was very jealous of Link and Zelda's relationship. When he became king he married Nabooru, and could only have daughters as a result. None of his children could have inherited the throne if Link and Zelda had a son. The Princess's Brother would have killed any person who stood between his daughters and the throne.
When Zelda had learned that she would bear a child, Link became very concerned. It was this concern that convinced the two to flee to Kokiri Forest where not even the Knights of Hyrule would be able to find them. Zelda died giving birth to the child, and Link stayed in the forest after informing the town that their princess had died along with the child. He raised Edgar in secret for as long as he could.
Link knew that Ganondorf was still a very real threat, but due to his circumstances he was too old to fight the King of Evil. He decided that his son would have to defeat the Prince of Darkness if he ever broke free. Link knew that the Triforce of Power had given Ganondorf insurmountable strength, but his Triforce of Courage felt powerless while the Triforce of Wisdom was lost. He knew that his son would be able to take up the mantle of the Hero of Time if the need arose, so he left his son a map with all the locations of the Spiritual Stones and Medallions for his son and a journal detailing Link's adventures throughout Hyrule and Termina as well as how to defeat all of the enemies Link had come across.