Reach the Secret Shop
If you didn't go to the secret shop earlier, here is how to reach it. Now that you know the Tune of Currents, you can get into the left side of the shop in Lynna City in the present time. Just go to Lynna Village in the past and stand above the trees at the top of the screen, then use the Tune of Currents to reach the closed off area in the present time. If you aren't positioned correctly, just move to different locations until you get there. This shop sells a piece of heart, a larger Ring Box, and after you buy the Piece of Heart you can buy rings.
Get the Hero's Sword
Go to the past and give Rafton the Magic Oar if you have it. He will give you the Sea Ukulele.
Still in the past, go to where the family is playing catch to the east of Lynna Village. Go one screen north, jump over the holes to the right and exit east, then exit south. Use the Switch Hook to reach a strange-looking man in a cave. Give him the Sea Ukulele to get the Broken Sword.
Now go back to Restoration Wall. One way to get there is to use the Tune of Currents to go to the present time, use a Gale Seed to warp to Symmetry Village, then activate a time portal to go back to the past. Use the southwest exit from the village, then walk west to the screen with the owl statue. Stand in the bottom left corner of the area and use the Tune of Currents to go to the present. Then follow the path to Restoration Wall. There will be a short set of vines that you need to climb along the way.
Climb the wall and go to Patch. He will do the ceremony to fix the Broken Sword, but the challenge is harder. The hardhat beetles move more quickly, and after you get rid of the first four, another set of four will appear. The easiest way to complete the challenge is to walk to one of the holes and let the beetles come toward you, then deliberately fall into the hole. You will reappear in the middle and the beetles will be clustered together near the hole, so it will be easier to push them all in. Once you complete the ceremony, you get the L-2 sword. It can shoot sword beams if you are at full health.
Find the Pegasus Seed Tree
Go to the present, warp to South Lynna, then go to Nayru's house and use the time portal next to it to go back to the past. Then go to where Nayru's house is in the present and go north, then west. Use the Switch Hook to reach a Goron cave. The Goron Elder is trapped under rocks and they need a bomb flower to get him out.
Go outside and, staying in the area to the left of the Switch Hook gap, use the Tune of Currents to go to this area in the present. The Gorons in the cave will say that the Great Moblin has built a tower that is preventing them from growing bomb flowers.
On the first floor, go to the east and use the stairs on the southeast. Then go west, then go to the bottom of the area and go all the way east to the stairs there. You can get 50 rupees.
Go back upstairs, then go west, then up to a set of stairs going up. Go up the small set of stairs here and follow the path around to a Goron. Bomb the cracked wall just below this Goron to get a Piece of Heart. Go back to the last screen and outside through the door in the south wall.
Once outside, go into the stairs on the left. The Goron here will mention that there used to be a tree in this area with seeds that would make you move quickly. Step on the switch to extend the bridge. Go across and go down the stairs to reach a chest with 30 rupees. Hop down the ledges and go back outside.
Go east until you reach an area with half of a Goron face carved into the wall. There is a rock on some white soil here that you can pick up to reveal a time portal. Use the Tune of Echoes to go to the past.
Go all the way west, then north to find the Pegasus Seed tree. Hit the seeds with the sword to get them.
Reach the Great Moblin
Now use the Tune of Currents to go back to the present time. Go south from where the Pegasus Tree is in the present, then go east to where there is a sign and a wide set of stairs. Go up to reach the Great Moblin's Tower. Use the left entrance.
Inside, go to the left and use a Pegasus Seed. You will temporarily move more quickly. Now go to the stairs at the top, then go up. At the top, you find the Great Moblin.
There are two small Moblins on the left and right who throw normal bombs at you. The Great Moblin will throw a large bomb at you. To hurt him, you have to throw the bomb back such that it explodes on him. However, the Great Moblin will throw the bomb back at you when you throw it, so you have to wait until just before the bomb explodes. After hitting him about three times, he moves much more quickly, so you have to wait until the bomb starts flashing and throw it as quickly as possible. To make it easier, try picking up the bomb as soon as the Moblin throws it, then carry it around until it starts flashing.
When the Great Moblin is gone, the Gorons will say that they can grow bomb flowers, and they will give you one. The Maku Tree will say that your name has appeared in Goron history.
Rescue the Goron Elder
There is a time portal to the east. Go back to the past and go to the Gorons who are punching the rock that has buried the Goron Elder. To get there quickly, go south from where the Great Moblin's Tower was in the present, then jump off of the ledge. Go into the cave and go toward the Gorons punching the rocks. They will use the bomb flower to break the rocks. The Goron Elder will give you a key.
Reach the Crown Dungeon
Go up through the cave where you rescued the Goron Elder. You'll reach the top of Rolling Ridge. Use the Tune of Currents to go to the present.
In the present, go to where the Great Moblin's Tower was. Go into the cave in the wall. Use a Pegasus Seed to jump straight up, then quickly jump to the right to avoid the green Zols. In the room to the east, you don't need to use Pegasus Seeds because there are small gaps that you can jump across to the door on the bottom right.
Outside, you will reach the locked door to the Crown Dungeon. Walk up to it to unlock it with the key that you got from the Goron Elder.