After Link obtains the Water Dragon's Scale, he swims into an underwater cavern within Faron Woods, leading into an underwater passage to the inside of the Great Tree. From here, he is able to exit at a higher point, then scale the Great Tree from the outside. Upon reaching the top, Link encounters Yerbal, a Kikwi hermit that helps Link to find Farore's Flame.
Later, on his search for the parts of the "Song of the Hero", Link finds Faron Woods flooded, and enters the Great Tree, which is now host to many Parella. At the top of its center, Link finds the Water Dragon, who has flooded the woods to stop the influx of monsters. When Link asks for Faron's part of the song, she tells him to find her many Tadtones before she will give it to him. After he has done this, she drains the water from the forest and she and the Parella leave the tree.