The Master Sword

After obtaining the three Spiritual Stones, play the Sun’s Song to make it night.

Swim towards the exit of the area and kill Gold Skulltula #31 on the wall located on a log to Jabu-Jabu's left before the entrance to the domain.

Head to Hyrule Castle. A cutscene (a non-interactive cinematic the game plays automatically) (a non-interactive story sequence) will play as you approach the drawbridge.

Swim into the moat to retrieve the Ocarina of Time.

Zelda will communicate with you via vision and teach you the Song of Time.

(Optional) Head back to Lon Lon Ranch and make it nighttime. Kill Gold Skulltula #32 on the window with your Boomerang.

(Optional) Go to the opposite end of the ranch and find Gold Skulltula #33 on the feed-silo outside.

(Optional) Return to Hyrule Field and head towards Kakariko Village, but do not enter. Just after the bridge, bomb the behind of a lone tree to the left of the entrance. Kill Gold Skulltula #34 on the wall inside.

(Optional) Head to Kakariko's House of Skulltula and claim the Giant's Wallet for collecting 30 tokens.

(Optional) Go to the Graveyard and collect Gold Skulltula #35 with the Boomerang.

(Optional) Plant a Magic Bean in the soft soil spot near the corner before leaving the Graveyard.

(Optional) Head to Kokiri Forest, behind the shop, and drop bugs in the soft soil spot to reveal Gold Skulltula #36. Plant a Magic Bean here for extra Rupees later.

(Optional - Normal Game) Enter the Deku Tree, drop into the basement, and head into the torch room. Use a block to reach a higher ledge and enter a crouchhole. Burn the web covering a path with a Deku Stick and a torch. Bomb the rock and enter the room. Kill Gold Skulltula #37 and pick up the token with the Boomerang. Exit the dungeon.

(Optional - Master Quest) Enter the Deku Tree and go to the back room on the higher level past the Big Deku Baba. Use a Bombchu on rocks on a high ledge. Climb up to find Gold Skulltula #2 (Master Quest). Return to the center room, drop into the basement, and climb to the high ledge to enter the crouchhole. In the torch room, find Gold Skulltula #37 (Master Quest) on the ceiling. Use the Song of Time to spawn blocks to reach it. Enter the northeastern room with the Big Deku Baba and claim Gold Skulltula #3 (Master Quest) on the wall. Exit the dungeon.

(Optional) Head to the Lost Woods with at least 40 Rupees. Turn left twice back towards where you found the Business Scrub. Drop bugs in the soft soil spot for Gold Skulltula #38.

Play the Song of Time in the Temple of Time to access the Master Sword.