Spiritual Stone

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Uses and Location
The Spiritual Stones are required to open the Door of Time, which has sealed away the Master Sword in the Temple of Time. When Link travels to Hyrule and meets Princess Zelda for the first time, she reveals that she had a dream that someone from the Forest in possession of the Kokiri's Emerald would come to meet her. She also reveals that the races who protect these stones will only open their minds to those who know the melody of the Royal Family.

During his quest to unlock the Sacred Realm and steal the Triforce, OoT3D: was denied the Spiritual Stones by each of their respective guardians. In response, he cursed them all. In order to obtain the Spiritual Stones, Link is required to free the guardians from Ganondorf's malevolence. Once all the Spiritual Stones are collected, Link must place them in the pedestal facing the Door of Time. He must then play the "Song of Time" in order to open the door leading to the Master Sword.

Kokiri's Emerald
The Kokiri's Emerald, the Spiritual Stone of the Forest, is protected by the Great Deku Tree. In order to obtain it, Link must destroy the parasite that had infested him.

Goron's Ruby
The Goron's Ruby, the Spiritual Stone of Fire, is a treasure hidden by the Goron race. After Link defeats the evil creatures inside Dodongo's Cavern, the Gorons' source of food, he is given the stone by Darunia, the patriarch of the Gorons.

Zora's Sapphire
The Zora's Sapphire, the Spiritual Stone of Water, is obtained by saving Ruto from Inside Jabu-Jabu's Belly, the princess falls in love with the hero and gives him the Zora's Sapphire as a symbol of their "engagement."

Trivia

 * During development of, the Spiritual Stones would be inserted inside the Ocarina of Time in order to enter the Temple of Time.
 * The Kokiri's Emerald was called "Kokiri's Jade" in early screenshots of the game, which is a direct translation from its Japanese name.