The next destination is to head back to Hyrule Castle to meet up with Princess Zelda now that you have all three of the Spiritual Stones. Before that though there are quite a few side quests that you can take care of.
Many of which are 
Gold Skulltula that you can reach at a distance now with the 
Boomerang. This guide will also take you through each of the Magic Bean locations which you should activate before proceeding to the Temple of Time (part of the Magic Bean Plant side quest).
The first Gold Skulltula is located in Zora’s Fountain though it will need to be night time. Use the Sun’s Song to switch from day to night if you need to. Go back up on to the log that Link and Princess Ruto were standing on when they transported out of the last dungeon. Across from the log on the west side of the rocks of the Fountain there is another Gold Skulltula to kill (number 34 of 100).
The next area that you need to travel to is the Kokiri Forest. You can travel there quickly by saving your game and hitting the reset button. You can also find a shortcut to the Lost Woods just outside of Zora’s Domain near the waterfall along Zora’s River.
Find the small mound of soil next to the shop and plant a Magic Bean in this location. Reenter the Lost Woods to find two more spots to plant the beans. The first one can be found by taking a left followed by another left past the Skull Kid.
The second can be found a good way into the Lost Woods. Take a right, a left, a right, a left and then another left to find the open area with the two Deku Scrubs that attack you. The soil is just behind the Deku Scrub.
The first Gold Skulltula to obtain is located in the first dungeon inside the Great Deku Tree. Return to the tree and use 
Farore’s Wind at the entrance in order to create a warp point to return to.
Drop down to the lower level - B1 on the Dungeon Map. The room that you are headed to is the room in the upper left corner. Climb the block and climb through the small passageway. There is a blocked passageway in the northwest corner of the room that you can use a 
Bomb on.
Destroy the wall and then kill the regular Skulltula on the far side of the room. The Gold Skulltula is on the southern wall and you will need to use the Boomerang to obtain it (number 35 of 100). Use Farore’s Wind again to return to the entrance of the dungeon.
There is a tree between the walls of Hyrule Castle and the entrance to Kakariko Village. Use the screenshot below to help you find it. Use a bomb to reveal a secret cave. There is a Gold Skulltula in the cave that you can now reach with the Boomerang (number 36 of 100).
Travel to Kakariko Village Graveyard at nighttime. There is another Gold Skulltula (number 37 of 100) on the southern wall that you can now obtain with the Boomerang. You should also take this opportunity to place a Magic Bean in the mound of soft soil in the Graveyard.
Travel up to the Windmill and go in through the doorway. There is a Piece of Heart in this room that is actually designed to be obtained later on in the game, but you can obtain it now with your Boomerang.
Stand on the spinning platform and climb on to one of the grey blocks that surround the platform. Aim carefully and use the Boomerang to pull the Piece of Heart Down.
Note: You can also swing by the House of Skulltula to pick up your next reward if you have picked up all of the available Gold Skulltulas up to this point. The next reward is a Giant’s Wallet.
Travel up the Death Mountain Trail until you reach the entrance to the Dodongo’s Cavern. Plant some Magic Beans in the mound of soft soil near the entrance and then go inside the Dodongo’s Cavern.
Take the platform that raises up to the second floor of the dungeon and proceed into the room on the east side. Drop down into the lower area and take the exit up the ladder on the southwest side of the room. Follow the pathway back through the main room of the dungeon and across.
You should find yourself back in a room with some statues that you can destroy and switch that you need to press. Press the switch and proceed into the next room. This will lead you into the room with the large set of stairs that you lowered by lighting all of the Bomb Flowers at the same time. Follow the pathway around on the left side to find some vines attached to the stairs that you can climb.
There is a Gold Skulltula that you can reach and kill now that you have the Boomerang (number 38 of 100). Exit the dungeon and head to the next destination which is the Lon Lon Ranch – just drop down to the lower level of the room to reach the exit easily.
Enter the Ranch at night and search for a Gold Skulltula hanging from the lit window of the house. Use the Boomerang to retrieve the token (number 39 of 100). Travel out to the silo to find another Gold Skulltula attached to the trees off to the right side (number 40 of 100).
Exit the Ranch and you can now complete the final portion of the Happy Mask side quest – click on the link below for more information:
Travel towards the west side of Hyrule Field before you venture back towards Hyrule Castle towards Gerudo Valley. Before you enter Gerudo Valley, search for a circle of stones just northeast of the entrance.
Place a Bomb in the center of the circle to reveal a secret hole that leads into a cave below. Use the 
Din’s Fire spell to remove all of the spider webs in the area. In behind the Lon Lon Cow is a Gold Skulltula on the back wall. Use your Boomerang to retrieve the token (number 41 of 100).
You can’t do too much in Gerudo Valley at this point primarily because the Gerudo Fortress, which makes up most of the map, is off limits. The guards posted out front will not let you pass by the gates.
Enter the Gerudo Valley at night time and search near the waterfall at the entrance to find another Gold Skulltula. Use your Boomerang to retrieve the token (number 42 of 100).
Note: Pick up some bugs from under the rocks in Gerudo Valley if you do not have any in your Bottles.
Grab the Cucco wandering around on the east side of the valley and peer over the edge of the cliff (on the southern side). A small cliff on the far side of the valley with a box on it will be visible. Use the Cucco to fly over to that platform.
Let go of your Cucco (hopefully without losing it – throw it into the cliff) and then roll into the box to reveal a Piece of Heart. Your Cucco will likely take off while you grab the Piece of Heart so jump off the platform into the river and follow it out to Lake Hylia. We are not done in the Gerudo Valley though.
There is another platform that you can reach with the Cucco. Float back down to the ledge with the single box-crate and the look north, on the west side of the shore. There is a large platform that you can reach. On this bottom ledge you will find a Lon Lon Cow, a Gerudo Guard and a mount of soft soil.
Place some bugs in the soil to cause a Gold Skulltula to appear (number 43 of 100). Plant some Magic Beans in the soil and then head to the north side of the platform.
There is a ladder located behind the waterfall that you can reach. Jump off of the northern side of the platform into the water and then climb the ladder. The ladder leads to a small cutout that contains another Piece of Heart. Purposefully follow the river out to Lake Hylia.
Search the southern section of the Lakeside Laboratory (by standing on the bridge) to find another Gold Skulltula clinging to the wall (number 44 of 100).
Make your way towards Hyrule Castle and a cutscene will begin as you approach. Note that you may have already initiated this cutscene if you already went to Hyrule Castle and this will not cause any problems.
The scene involves Princess Zelda and Impa making a hasty escape from the Castle with Ganondorf in pursuit. Jump into the moat once the scene ends to retrieve the 
Ocarina of Time that Zelda threw in Link’s direction.
The game will cut to another scene where Princess Zelda will teach link a new melody called the Song of Time.
Travel to the Happy Mask Shop first if you spoke to the Running Man and completed the Happy Mask side quest. Click on the link for more information:
You can now proceed to the Temple of Time, but before you do, make sure that you have completed everything that you can up until this point. You should have:
Gold Skulltula tokens obtainedDin’s Fire and Farore’s Wind)Revisit any of the side quest pages listed above if you need help completing any of the listed items. Once you are ready to go, proceed to the Temple of Time which is located to the right of the Happy Mask Shop in Hyrule Market.
Walk up to the red carpet in front of the pedestal and the inscription provides a clue on what to do next: “Ye who owns 3 Spiritual Stones, Stand with the Ocarina of Time, And play the Song of Time”.
Pull out the Ocarina of Time and play the Song of Time as instructed and the three Spiritual Stones will appear. The doorway at the back of the Temple will open up allowing Link to enter.
Enter the back of the Temple and Navi will point out that the 
Master Sword is inserted in the stone in the center of the room. Walk up to the Master Sword and pull it out of the pedestal to initiate another cutscene.
Link will be transformed into an adult after remaining trapped in the Temple of Time for 7 years. Breaking the seal on the Master Sword also allowed Ganondorf to enter the Sacred Realm and become the King of Evil, which means that many of the places you visited previously will have changed.
Attempt to exit the Temple of Time and you will be interrupted by Sheik. Sheik will tell you that the first place you should visit is the Forest Temple, but there are a number of things that you can do now as adult link. Check out the next page for more information.
