Great Deku Tree

The Great Deku Tree is the fatherly guardian of the forest who safeguards not only the dense land around him, but the small population of beings that live in his shadow. In Ocarina of Time, the famed Kokiri praise and worship the massive tree, sharing a home in the Kokiri Forest, while in The Wind Waker, these beings are none other than the Koroks, timid wood creatures who live collaboratively with the talking tree in the arboretum that is the Forest Haven.

Ocarina of Time
The Deku Tree made his first appearance in Ocarina of Time as guardian of the Kokiri and of their forest. He protects the Kokiri's Emerald, one of the three Spiritual Stones.

The Deku Tree was cursed by Ganondorf in Ocarina of Time, and embarked Link on a quest to save Hyrule. The Great Deku Tree tells Link the story of the three Golden Goddesses and how Hyrule and the Triforce were created. He died shortly after telling Link to go save Princess Zelda. When he died, a seed fell from one of his higher branches to the ground. After defeating Phantom Ganon as an adult, Link goes back to find a new Deku Tree Sprout growing in front of the old Deku Tree.

The inside of the Deku Tree is also the first dungeon Link must get through in Ocarina of Time, the boss of the dungeon being Queen Gohma.

It is possible that the Deku Tree became the Forest Temple of Twilight Princess, seeing its striking similarities to the appearance of the Temple.

Deku Tree Sprout
The Deku Tree Sprout is the successor to the Great Deku Tree as the protector of the Kokiri Forest and by extension, Hyrule itself. He appears in Ocarina of Time after Link has defeated Phantom Ganon and received the Forest Medallion from Saria with the words, "Hi there! I'm the Deku Tree sprout!" He tells Link the story about Link's past and how Link's mother came into the forest and delivered Link into the Deku Tree's care. He then urges him to complete his quest and defeat Ganondorf.

The Wind Waker
The Great Deku Tree acts as the guardian of the Forest Haven, which is home of the Koroks. To them, the Great Deku Tree is considered a father figure to the children of the forest, for it is him that protects them from evil. One thing that set the Deku Tree of the Great Sea apart from his predecessor was that each year, the Great Deku Tree would send off some of the Koroks to plant trees all throughout the islands. This was done in the hope that, as the forests spread and the trees grew, they would consolidate the remaining land above the Great Sea, and allow some of the land lost during the Great Flood to be reclaimed from the depths. It also rejuvenates his power, for if his power were to wane, the life of the Koroks would fade as well.

When Link first meets the Great Deku Tree, hordes of ChuChus are invading his face. After the young hero eliminates all of them, the Great Deku Tree mistakes him for the legendary Hero of Time due to his clothes, and begins to speak the ancient Hylian language. The Great Deku Tree realizes his error, and it is then that he realizes why Link is there: to receive Farore's Pearl from him. Just as the guardian of the forest is about to begin the annual Korok ceremony in order to give the pearl to Link, Linder informs the Great Deku Tree of Makar's accident, and the ceremony is called off. After Link rescues Makar from the depths of the Forbidden Forest with the help of the Deku Leaf given to him by the Great Deku Tree himself, the ceremony begins, and in return, the Great Deku Tree hands over Farore's Pearl, as promised.

It is possible that this Deku tree grew from the Deku Tree Sprout in Ocarina of Time, and that the Forbidden Forest is the remains of the old Deku Tree.

Freshly-Picked Tingle's Rosy Rupeeland
The story of the Great Deku Tree in Freshly-Picked Tingle's Rosy Rupeeland is somewhat similar to that of the one from Ocarina of Time. Due to pollution, the Deku Tree Sprout is dying; while at the same time, the Great Deku Tree is also nearing his end. When Tingle met them, the Great Deku Tree asked if he would enter him and retrieve forest water, which could cure the Deku Tree Sprout. Tingle accepted and entered the Deku Temple. After defeating Bana Bana, Tingle obtained the water and rushed back to cure the Deku Tree Sprout. After that, the Great Deku Tree died happily, but not before paying Tingle for his service.

Parallels

 * In Holodrum and Labrynna there are talking trees, similar to the Deku Tree, known as the Maku Trees; there is both a male tree and a female tree.
 * Other tree-dungeons can be found in: The Legend of Zelda (Eagle Labyrinth), Oracle of Seasons (Gnarled Root Dungeon), The Wind Waker (Forbidden Woods), Twilight Princess (Forest Temple), and Spirit Tracks (Forest Temple).

Manga

 * In the Ocarina of Time manga, there is another talking tree known as the Baga Tree. He lives in the Lost Woods and has never beaten the Great Deku Tree. The Bagu Tree always wanted to destroy the Great Deku Tree. The rumor that if one gets lost in the woods, one turns into a Skull Kid is true, as that is what the Bagu Tree does to them. He is later killed.
 * The manga also depicts a Gossip Stone, which says the Deku Tree is troubled because he cannot scratch his own back.