Hyrulean Civil War

Known History of the War
According to The Legend of Zelda: Ocarina of Time, there was a fierce war in the realm of Hyrule shortly before the events of the game. While trying to escape from the fires of the war, a Hylian mother and her baby boy entered the forbidden Kokiri Forest, although the mother was gravely injured in the process. As she was dying, her only choice was to entrust the child to the Great Deku Tree, the guardian spirit of the forest, who could sense that this was a child of destiny whose fate would affect the entire world. After the mother passed away, the child was raised as a Kokiri, not made privy to his true heritage until the Deku Tree Sprout revealed the true story to him years later, when the boy grew up to become the Hero of Time.

Possible Origins of the War
The Hyrulean Civil War or Unifying War was a conflict that occurred shortly before the events of The Legend of Zelda: Ocarina of Time. While the war's history is not entirely clear, its history can be pieced together with careful study of the texts and cutscenes that appear throughout the series. What is definitely known (via OoT) is that it resulted in the unifying of the country of Hyrule under one banner and that it occurred shortly before the outbreak of the Imprisoning War, orphaning the child that would grow up to become the Hero of Time and leaving him under the guardianship of the Great Deku Tree. It can be surmised from Link's age at the time of The Legend of Zelda: Ocarina of Time that it occurred about ten years prior to OoT's events, as Link was noted to have been born during the war and orphaned as a result of it. It can also be surmised that Ganondorf's service in the war earned him some standing with the King of Hyrule (which he put to good use at the opening of the Imprisoning War), as the King was not so quick to believe Princess Zelda's accusations concerning Ganondorf's treachery without concrete proof, seemingly trusting him. It was noted in the opening cutscene of The Legend of Zelda: A Link to the Past that there was a war between the tribes of Hyrule over the Triforce at some point in Hyrule's distant past ("...the people began to quarrel and fight..."), and seeing as this war lead almost directly to "evil power flowing from the Golden Land," it can be surmised that this particular conflict it was describing was the Hyrulean Civil War that took place shortly before Ganondorf unleashed the Great Cataclysm and sparked the Imprisoning War. It was noted that the Triforce had become a desireable object amongst Hyrule's tribes in ALttP, and that somehow the fierce fighting broke out amongst them over it, meaning that at some point one of the tribes most likely threatened to seize it for their own. We know from The Legend of Zelda: Twilight Princess that the ancestors of the Twili, the Dark Interlopers, tried to do just that, which would make perfect sense as to what catalyst triggered the civil war. The presence of the Temple of Time in TP also suggests that the game occurred within a century following OoT, lending credence to the possibility that the story of the Twili's banishment to the Twilight Realm occurred around the time of OoT. With this information, it is possible to discern roughly when, how and why the war took place and under what conditions. A possible (although not certain), more collective synopsis of the conflict, as pieced together from information gathered throughout the series, follows:

Ten years before the events of The Legend of Zelda: Ocarina of Time, a group of Dark Interlopers (the Twili) attempted to use their dark magic (in the form of a relic known as the Fused Shadows) to seize control of the Sacred Realm and the Triforce that was held within it. Upon learning that one tribe was trying to take the Triforce for themselves, the other tribes of the land of Hyrule began to quarrel and fight, as depicted in the opening sequence of The Legend of Zelda: A Link to the Past, leading to a massive civil war that engulfed the entire land. The three Goddesses of Hyrule sent the Light Spirits to drive the Dark Interlopers into a realm known as the Twilight Realm, as depicted in The Legend of Zelda: Twilight Princess. They also sealed away the Fused Shadows within the Great Deku Tree (later to become a successor Forest Temple), the Fire Temple (later known as the Goron Mines), and the Water Temple (later known as the Lakebed Temple). As the civil war raged across Hyrule, the Gerudo King of Thieves, a man named Ganondorf, came to help the King of Hyrule unify the land and to quell the destructive war that was tearing the land apart. As a result, the Hylians were able to end the war with Ganondorf's help, and Ganondorf won the King's trust. It was due to this war that Ganondorf learned of the sacred Triforce and the power it represented, which he would covet not so long afterward in another even greater war known to legend as the Imprisoning War. During the course of the war, a Hylian mother tried to escape the fighting with her infant son, but was gravely injured in the process. As she fled to the Kokiri Forest, her time grew short, and her only choice was to entrust the child to the Great Deku Tree, the guardian spirit of the forest. The Deku Tree could sense this was a child of destiny, whose fate would affect the entire world. After the mother passed away, the child was raised as a Kokiri, completely unaware of his lineage as a Hylian and descendant of the Knights of Hyrule or of his destiny as the Hero of Time that would come to pass in due time when Ganondorf returned to Hyrule a decade later.