Link makes his way up Zora’s River towards Zora’s Domain, the source of all water in Hyrule and the location of the final Spiritual Stone. When Link arrives the Zora’s are in disarray and their King is despondent because Princess Ruto has gone missing.
After considerable investigation, Link discovers that Ruto is somehow inside Lord Jabu-Jabu, the patron deity of the Zora’s. Allowing himself to be swallowed whole, Link enters the belly of Lord Jabu-Jabu, eventually finding Princess Ruto in the middle of a search to recover a lost item.
Recovering the item, which just so happens to be the Spiritual Stone of Water, and defeating the Bio-Electric Anemone: Barinade, Link and Ruto are able to leave Lord Jabu-Jabu. Three spiritual stones in hand, Link makes his way to Hyrule Castle to meet with Zelda.
But a dark cloud looms over Hyrule Castle, suddenly an all too familiar scene unfolds before Link. Zelda and Impa ride out of town, Zelda catches sight of Link and tosses an object towards him. Hot on their tail is Ganondorf. Link makes to stand against him, but Ganondorf is clearly a powerful magic user and casts Link aside, proclaiming he will soon rule the world, and resumes his chase.
Now alone, Link recovers the thrown object which fell into the moat around Hyrule Castle Town, discovering it is the Ocarina of Time. A telepathic message from Zelda tells Link that she had to leave the Castle, and teaches him the song Song of Time, the final piece necessary to opening the door to the Sacred Realm.