Meeting at the Temple of Time
Before you head to the Temple of Time, there is one side quest which you can now fully complete. Travel to the Zora’s Fountain (where the Ice Cavern is located). One quick way to get there is to warp to the Shadow Temple using the Nocturne of Shadow and then travel up the Zora’s River using the Magic Bean Sprout.
Travel to the southwest corner of the Fountain and look for a large grey boulder sitting in front of the pathway leading into the Great Fairy’s Fountain. Lift the grey stone out of the way (which you can do now that you have the Silver Gauntlets) and drop down the hole. Equip and use your Lens of Truth as there are a multitude of Skulltulas hanging from the walls which you will need to defeat or dodge as you head up the pathway.
Climb the ladder at the end of the path and kill the last Skulltula which can be seen without the Lens of Truth. Use the Longshot to kill the last Gold Skulltula and pick up the token (number 100 of 100). You are now completely done the Gold Skulltula side quest! Congratulations!
Check out the page below if you are actually missing some of the Gold Skulltulas or for more information about the rewards for completing the quest.
House of Skulltula (100 of 100 Gold Skulltulas)
The Gold Skulltula side quest is now complete - but the reward is pretty lacklustre. Travel back to Kakariko Village to finish the quest.
Return to the Temple of Time to initiate a cinematic involving Link and Sheik. Sheik will tell you a short story about the three goddesses and the Triforce and then will reveal that he is actually Princess Zelda in disguise.
Princess Zelda will tell you that she currently possesses the Triforce of Wisdom, while Ganondorf possesses the Triforce of Power and Link possesses the Triforce of Courage. Princess Zelda will provide Link with the Light Arrows which are needed to defeat Ganondorf.
Make your way to Ganon’s Castle.