After rescuing the Maku Tree in the past, you return to the present and learn from the Maku Tree that you must gather the Essences of Time.
From the Maku Tree's grove, go south and burn the small tree there using an Ember Seed. You will find a chest that contains 30 rupees.
Bipin and Blossom's Son
In town, you can go into the house east of where Ambi's Palace was in the past to meet Bipin and Blossom. They have a newborn son and Blossom asks you to name him. You can name him whatever you like. Your interactions with Blossom and the son will affect the type of child and adult he grows into. See the Bipin and Blossom's Son Guide for more information.
Prepare for Yoll Graveyard
You might want to go buy a shield from the shop in town before heading to the next dungeon, although you can get a cheaper one later on.
Exit town to the east, then go north to the screen where you pushed the block with the triangle mark in it. Go east from here, then south. Burn the small tree with an Ember Seed, and go east.
Enter the Graveyard
Burn the second tree in your way, then exit to the east. Go south down the small set of stairs, then in the screen with the ghost, exit to the left. You will find three boys talking about the ghost in the grave under the tree.
Go down the bridge, then go east until you find the two small trees. Burn the one on the bottom with an Ember Seed and go down the stairs. Go up to each lantern and use an Ember Seed on each one to make the Graveyard Key appear. Go get the key, then go back upstairs.
Go back to the screen with the ghost, then go north twice and walk through the lock in the gate to unlock it. Go around the path beyond the gate, being careful of the crows that fly at you from the trees. Go down the bridge and into the dungeon entrance to reach Spirit's Grave.