- "One day, to escape from the fires of the war, a Hylian mother and her baby boy entered this forbidden forest. The mother was gravely injured... Her only choice was to entrust the child to the Deku Tree, the guardian spirit of the forest. The Deku Tree could sense that this was a child of destiny, whose fate would affect the entire world, so he took him into the forest. After the mother passed away, the baby was raised as a Kokiri. And now, finally, the day of destiny has come!"
- — Deku Tree Sprout
During the Hyrulean Civil War, Link's Mother was gravely injured, and gave her son to the Great Deku Tree, in order to protect him from becoming another casualty of the war. The Great Deku Tree took him in, sensing he was a "child of destiny", and raised him as a Kokiri. Despite attempts by the Kokiri to tend her wounds, she died shortly after.
Link's Mother rides initially on horseback. When she reaches Kokiri Forest, just as she is about to faint, she hears small footsteps nearby and loses consciousness as many small figures appeared from the shadows of the trees around her. These small figures are the Kokiri, the child-like race protected by the Great Deku Tree, whose members are said to never age. They bring Link's Mother to their settlement deep within the forest and attempt to tend to her wounds, but her injuries are so great that they could do little but comfort her. They then take her before the Great Deku Tree himself, the guardian spirit of the forest that takes the form of a giant, talking tree. The Hylian mother regains consciousness as her last moments were nigh, and the Deku Tree converses with her concerning the future of her son. Knowing that her time is quickly drawing to a close, she reveals the child's name to be Link and makes it clear she does not want him to become another victim of the civil war that was tearing the realm apart. Her only option is to leave her child under the guardianship of the Great Deku Tree, who could sense that her child was one of destiny, whose fate would affect the entire world and change the course of Hyrule's future in years to come. Shortly after the Great Deku Tree promises to protect her child from harm and to watch over him as he grows.
Following the burial of the Hylian mother, the Great Deku Tree resolves to raise Link in accordance with Kokiri tradition, teaching him the means necessary to survive in the forest and to deter him from straying outside its borders until he was ready. The Great Deku Tree decided to not tell the child of his true heritage or what he truly was until the time was right and he was ready to know. The one problem with this omission of information, however, is the fact that every Kokiri has a fairy companion to accompany them throughout the course of their lives, meaning Link, not actually being Kokiri, was the only member of the tribe without one. For approximately ten years, the boy grew up amongst the children of the forest, not having any idea why he seemed somehow different from all the other Kokiri, nor why he alone did not have a fairy companion (he was referred to as "The Boy Without a Fairy", by the other children). Thus, the boy that would one day become one of the greatest figures in Hyrule's history vanished from the public eye, disappearing into the depths of the forest, not to be seen nor heard from again, for over a decade.
German Club Nintendo Comic
In this prequel comic to Ocarina of Time exclusive to the German Club Nintendo magazine, Link's Father discusses with his Mother and Grandmother (on his Mother's side) where to bring Link to avoid the incoming Hyrule Civil War. Link's Grandmother recommends the Kokiri Forest based on legends she heard, and the couple agrees to bring Link to the area the next day. However, Link's Father dies protecting the King of Hyrule later that night, and Link's Grandmother encourages her daughter to go without her.
Before entering the forest, she runs into Kaepora Gaebora, who encourages her to take her son to the Great Deku Tree and warns her that any mortal who enters the forest is doomed to become a plant. She persists regardless and reaches the Deku Tree. The tree tells her that her child will play a very important part in the future of Hyrule, but she doesn't believe him. To her, Link is merely an ordinary baby. The Deku Tree accepts Link, but his mother dies and is turned into a tree once the Kokiri take him in.
Link's Mother is a woman named Medilia, who lives in Calatia with the rest of Link's family.
Link's Mother is The Queen of Hyrule
Due to Link and Zelda sharing similar character designs and ages in Ocarina of Time, and Zelda not having a present mother and only a father, it is possible Link's mother was the Queen of Hyrule who fled and died during the war while Zelda was left with Impa. This would also explain Link's mother knowing where the Deku Tree was.
Link's Mother Became a Stalfos
It is possible Link's mother became a Stalfos since she passed away in Hyrule's forest, however since it was near the Great Deku Tree it also could of not have happened.