Game Boy Advance only:
Link, a hero from the land of Hyrule, has seen much evil appear in a short time. Not long ago, his destiny changed, and he became a mighty force of good, defeating the Evil King Ganon, rescuing Princess Zelda, and restoring peace to the kingdom of Hyrule. Ganon sought out a force, that of the Triforce, and could not obtain it all. Instead, that very force was split into three parts: Power, Wisdom and Courage. One of those parts, Courage, is within Link. Another, Wisdom, lies in Princess Zelda. Ganon held the last force, Power, but it was lost upon his demise. However, an evil sorcerer is about to appear, and has plans that could re-awaken the dark power Ganon held...
Forest of Time
Talk to all the animals: the bear will move aside so you can fit through. A guy in blue, Ralph, recognizes you as being from Hyrule and then introduces you to Nayru. She tells you that she feels that danger is approaching the land.
Suddenly, Veran, Sorceress of Shadows attacks and takes possession of the body of Nayru. Then, she escapes through a time portal.
Head north from the shop. Enter the building marked with a . Vasu gives you a L-1 Ring Box. He also gives you a Magic ring and teaches you how ring appraisning (i.e. identifying) works. Once identified it turns into the Friendship Ring. Most Rings will have some sort of power, but they can only be equipped after being identified.
Leave the jewelry and continue north. Head through the marked door into the Maku Path. Keep heading north until you reach the stairs, then go up them. You have found the Maku Tree! She explains more of what's going on... and then she vanishes! Head east. Ralph jumps into the portal Veran left. Follow him when you're ready.
400 years earlier
Head south, then west in Lynna village, then south again. Enter the left door on the building to play a minigame for 10 Rupees. If you score more than 350 points there, you'll get a Magic Ring.
Notice the right-hand door on the building. If you're playing on a Game Boy Advance you'll be able to enter (otherwise it's locked) and buy two Magic Rings (any ring from Class 3 and GBA Time Ring) and a Gasha Seed for 100 Rupees each. Once you've got the Shovel, keep digging until you have enough Rupees.
Anyway, head all the way west then north. Enter the house and talk to Pippin for a Gasha Seed. Head back outside and then south. Press on the bordered square of soil and plant the seed. It will now progressively grow the more you do. Keep checking it now and then to see if it has grown a nut. When it does you will get a Magic Ring, or maybe even a Piece of Heart!
The Black Tower
Now head all the way south and follow the path around until you reach the entrance to the Black Tower. Talk to the man in the doorway and he'll explain the origins of the tower. He then moves aside, so go on in.
Follow the path counter-clockwise until you see some holes and a guy reading something. Talk to him to get the Shovel! Now you can dig holes and clear piles of rubble. Start with the ones to the right: break through them and then head south to exit. Go back outside. Dig through the rubble to claim your first Piece of Heart. The Shovel enables you to dig in soft earth in search of Rupees and other treasures.
Now go back at the entrance to the village (out of the tower, then head north, east three screens, and finally north). You can now dig your way into the Maku Road.
DUNGEON: The Maku Path
Head north, push the block up to open the door and continue north. Push the block to the left or right. The bats are known as Keese. Anyway, head east. Kill the Gels and the doors open, so head north.
Push the block up and head left. Push the left block up and the right block right. Step on the button and a chest appears. Head back to the doorway and then follow the path left to reach the chest, which contains a Small Key. With the Small Key in hand, return to the room with the Keese and unlock the west door.
Go between the two formations and push the center-left block inwards, the one above it up, and the one below the button to the right. After stepping on the button the door opens. Do the same on the other side to find a hidden Stairs which leads to 30 Rupees.
In the next room are some Stalfos skeletons. Push the bottom-left block up and the bottom-right block left to claim your second Piece of Heart. Now go right and push the solitary block in any direction to open the door. Continue east, then north and up the stairs.
The Maku Tree
Two Moblins (pig warriors) are attacking the Maku Tree. Kill them and the Maku Tree will thank you for saving her. When you leave, she says that she wants to marry you. Okay... continue south and step into the time portal in front of you.
Back to the present
Head north and you will notice that the Maku Tree has reappeared. She explains that you need the eight Essences of Time in order to beat Veran. She also gives you the Seed Satchel including 20 Ember Seed, enabling you to pick seeds from trees dotted around the land.