Instructions
Fight and kill the monster that has taken over the Great Deku Tree. Link travels through the Great Deku Tree early in the game---return to this area and use your sword and other equipment to kill the monster. Aim for the monster's weak point (as identified by your on-screen guide, Navi). Once you have defeated him, you will be rewarded with the first spiritual stone---Kokiri's Emerald.
Travel to Dodongo's Cavern and clear the area of all monsters, including the end-level boss. The entrance to the cavern is located near Kakariko Village, which is another location Link visits early in the game. Your on-screen guide will once again point out weaknesses in enemies for you to kill. Clearing the area of all monsters sees Link rewarded with the second spiritual stone---Goron's Ruby.
Travel to Zora's Fountain, which is an area near the "Zora's Domain" location marked on your map. Enter into the stomach of the great beast Lord Jabu-Jabu. Kill all enemies inside Lord Jabu-Jabu to be rewarded with the third and final spiritual stone---Zora's Sapphire. With all three stones together, Link can now begin the "time travel" portion of the game.