After you complete the Ancient Ruins dungeon and receive the Essence, the Maku Tree says to go to the Graveyard west of Horon Village. However, to get there you need to find a way across the sea.
Meet the Piratian
Go to Horon Village and exit east from the village. Go into the hollow log to the south. Go east until you reach the gate with the skeleton pirate. Talk to him.
Go to Subrosia
Go back to Horon Village. Go south from the fountain and go down the stairs. If there are no stairs here, burn the trees. In the underground room, use the Magical Boomerang to hit the switch and extend the bridge, allowing you to reach the portal to Subrosia. Use it, then go down the stairs.
Talk to the pirate on the right. He will push the drawers according to a
pattern. The pattern is:
3, 3, 2, 1, 1, 4, 4, 4.
Go downstairs and talk to the pirate captain, who asks you to look for the bell. Go back upstairs and go into the vortex back to Horon Village.
Exit east from Horon Village and go into the hollow log to the south. Walk east on the beach and talk to the pirate. He will leave because you promised the pirate captain in Subrosia to look for the bell. Push on the gate skulls in the same order as the pattern shown by the Piratian in Subrosia. This will open the gate.
Find the pirate ship in the center of the desert. Go down the stairs. Talk to the ghost pirate, who says to find his skull in the desert.
Go to the northeast corner of the desert, where there is an oasis. Talk to the pirate's skull, then pick it up with the Power Bracelet. Go around the desert and carry the skull close to the centers of quicksand pits until the skull starts opening and closing its mouth. Keep carrying the skull and sink into the quicksand pit that it reacted to.
You should end up underground. Get the red object up above. It's the rusty bell. The skull moves on to the afterlife. Go upstairs and outside.
Go back into the pirate ship in the desert. Push the brown crate up, then go north and up the stairs. You end up in Subrosia.
Give the Captain his Bell
Go west from the Subrosia pirate ship, through the Subrosia graveyard. Go into the pirate house and talk to the captain. He says it's too rusty and tells you to go get it polished.
Go to the Subrosian Smithy. Talk to the guy behind the counter and say "Do it!" when asked. You will receive the Pirate's Bell.
Go back to the pirate captain and give him the bell. The Piratians will fix the ship and set sail. After getting seasick, the captain will decide to put ashore.
Go north from the ship and into the house. Open the chest to get bombs. Use a bomb on the cracked wall on the right. Go through and go outside. Change it to summer.
Go back south from the house and then go west. Ignore the cave and continue west. Plant a Gasha seed if you wish, then climb the vines. Go north and go down the stairs to enter the next dungeon, Explorer's Crypt.