The Great Deku Tree is the guardian deity of the Kokiri and Kokiri Forest. It is located just through a tunnel from inside Kokiri Forest, although Link is stopped by Mido before allowed access to it. After obtaining a sword and shield, he is allowed pass Mido and goes to talk to the Great Deku Tree. When he first meets with the Deku Tree, Link is told a story about how the "man in black armor" is going to cause great destruction and evil.

The Great Deku then tells Link to go inside and get rid of all the monsters, which is the first dungeon of the game. After traversing the dungeon and defeating Queen Gohma, Link receives the Kokiri Emerald from the Great Deku Tree. The Great Deku Tree then tells Link that he is withering away due to a curse placed on him by Ganondorf, telling Link to go to Hyrule Castle and meet with the "princess of destiny." After Link is trapped in the Temple of Time for seven years and defeats Phantom Ganon in the Forest Temple, a Great Deku Sprout shows up where the Great Deku Tree is located.