At the end of Ocarina of Time, Link defeats Ganon and saves Hyrule, but then is sent back to his time as a child by Zelda. Having proven himself worthy of the Triforce of Courage, he returns to the young Zelda at Hyrule Castle and they are able to prevent Ganondorf from launching a successful attack on Hyrule.
Some time later, Link decides to venture into the Lost Woods to look for Navi. He is attacked by the Skull Kid and chases him into a portal that leads to Termina, where he must repeat time until he can stop the Skull Kid. Eventually he returns to the Lost Woods. The events in Majora's Mask are ambiguous and it is not known for certain if Termina actually exists. Evidence seems to suggest that Link does eventually make it out of the Lost Woods, however.
One theory also suggests that Link eventually marries Malon and that their descendants inherit the lifestyle of ranchers, among whom is the Link from Twilight Princess.
Now, at some point, whether before or after the events of Majora's Mask, Ganondorf is finally captured and sentenced to death for his crimes. The original six sages carry out the execution, but Ganondorf survives due to possessing the Triforce of Power (probably because Link had returned from the future with the power of the Triforce of Courage, causing the Triforce to already split) and kills the sage of water. They then banish him into the Twilight Realm with the Mirror of Twilight as a last resort. Along with the banishment of Ganondorf, the Gerudo also dissapear, scatter, or are killed off, leaving the Gerudo Desert empty. In fact, this might have already happened prior to Ganondorf's banishment.
Centuries later, Ganondorf was able to free himself from the Twilight Realm with the help of Zant. Remember, this version of Ganondorf had never been defeated by any Hero, only banished by the sages. But he still wants to rule Hyrule, and knows that he doesn't have the full Triforce. He captures Zelda, thinking that she possesses the Triforce of Wisdom, but is eventually confronted by Link and Midna. He converses mostly with Midna, calling Link only her "little friend". But in the ensuing battle he soon realizes that Link is a formidable foe, and, after defeating Midna, eventually engages him in a duel. But Link defeats him with the Master Sword, and Midna is restored by the Light Spirits. She later shatters the Mirror of Twilight before returning to her own realm.
While the events in Hyrule Warriors may occur in a sort of alternate timeline, the period in which they would happen takes place after the Era of Twilight. In this period of Hyrule, Ganondorf's soul had been split into four pieces and sealed away within different locations and times. One of these soul fragments was sealed away by the Master Sword itself in the Temple of the Sacred Sword, which may be what was once known as the Temple of Time. The Triforce having been restored, it is watched over by the Guardian of Time, a sorceress. This sorceress, who was fascinated by the spirit of the Hero of Legend, fell victim to a dark influence that entered her heart. Corrupted by it, she proceeded to open portals to the eras in which the various soul fragments of Ganondorf had been sealed, allowing monsters to flood Hyrule. A new hero rises, Link, becoming worthy of the Triforce of Courage, and it is up to him and others to repel the forces of evil and defeat Ganondorf once again.
The overworld map of this game doesn't entirely make sense, but if we ignore that, then there are some interesting details to gain. For example, the Gerudo Desert is still abandoned and there are no signs of any Gerudo, supporting the idea that the Gerudo were killed off or fled ages ago.
The Great Deku Tree is present, but has long since died of Gohma's curse. Forts and villages have been built up around it, and it is still revered. There is no sign of the Kokiri, also suggesting that they were a temporary form of the Korok. And like in Twilight Princess, the Korok are also not present.
Gorons are still around and have maintained good relations with the Royal Family. Apparently, the Sheikah have somehow persisted, as is evidenced by Impa, a royal guard and commander.
