Go to Ambi's Palace

Go to Ambi's Palace. It's in the past, just north of Lynna Village. Ralph is outside and he will mention a hidden passage in the garden.

Open the Hidden Passage

Go into the palace. There are some screens to the left and right where you must avoid the palace guards and step on a switch. Use Pegasus Seeds in the bottom right area to quickly run down to the switch.

After stepping on all four switches, the statues to the right will be moved out of the way and you can cut the bushes to reach the hidden passage. Go down the stairs.

Reach Nayru

Dive into the water. Swim west, avoiding the whirlpools. In the last room, swim onto the lighter tiles and go to the surface. Go up the stairs in the corner.

Push a block out of the way and go through the eastern exit. If the guards see you in here, just use a Pegasus Seed to outrun them and go to another room. Or you can just hit them repeatedtly until they run away. Avoid the guards to go north and open a chest that contains a ring.

Go back to the room where you first arrived in the palace and use the west exit this time. If you need health, exit north to find some fairies. Otherwise, go up the stairs.

Make your way east past the guards. In a room with no guards and two areas of water, go north.

Possessed Nayru

Hit Nayru with a Mystery Seed to separate Veran from her body. Use the Switch Hook to move Veran farther from Nayru's body. Then hit Veran with your sword. You can't block the fireballs, so just step between them. Repeat this three times to liberate Nayru.

You will learn the Tune of Ages, which allows you to go back and forth in time without needing Time Portals.

After the cutscene, the Maku Tree will say that the next Essence is in a fish.

Now that you have the Mermaid Suit, you can swim in the ocean. You can also dive into the ocean. There are underwater areas that you can swim around in.

Get a Shield Upgrade

Swim to the area northwest of Crescent Island in the past. There is a narrow corridor that you can use to swim along the west side of Crescent Island toward the south. Here you can reach a spot southwest of Crescent Island where you can see a cave entrance in the water and a time portal on the island. Dive down into the ocean and swim to the right, then go back to the surface. Swim into the cave to get an upgraded shield from the Tokay.

Reach the Zora Village

Go to the present day and swim southwest from Crescent Island. There will be a treasure chest blocked by blobs in the water. Go to the screen north of that. You will find a house there where the woman inside says that the island drifted to the west, so it was farther east in the past. Go outside and use the Tune of Ages in front of the house.

Swim west and then go north onto the ledge. Use the Tune of Ages. Go underwater and swim east. Use the Switch Hook to go to the right. Swim to the right, then go to the surface. Get on land and use the Tune of Ages. Swim west as far as you can go. Go south when necessary and onto the ledge. As soon as you climb up, use the Tune of Ages. Then go underwater and swim south, then use the Switch Hook to go across. Go west.

Get a Gasha Seed

Go to the west side of the village where you can see a treasure chest, and go to the surface. You can reach the chest containing the Gasha Seed by going over the land and then diving down on the other side.

Get a Ring

Go to the northeast part of the Zora Village and go to the surface. Swim northeast to find a chest that contains a ring.

Add a Warp Spot

Above the water, in the area south of where the throne room is in the Zora Village, you can find a Gale Seed tree. Make sure to look at it so it gets added to your list of warp points. The tree exists there in both past and present.

Save King Zora

If you do not have a Potion, go to Yoll Graveyard and swim across to the tree hut in the northeast corner and buy a potion from Syrup. Then warp back to the tree near Zora Village (see above paragraph for how to find this tree). Go to the past, then go underwater to the Zora Village and go to the throne room and give King Zora the Potion.

Get 200 Rupees

Go to the present day and go to the throne room. There is a chest on the lower level that contains 200 rupees.

Get the Library Key

Talk to King Zora in the present time and agree to find out how to help Jabu-Jabu. The king will give you the Library Key.

Enter the Library

While underwater, swim east from the throne room and go as far east as you can go. Then go to the surface, go up the stairs, and go east. You will find the library. You can't unlock it in the present, but use the Tune of Ages to go to the past and unlock the library there.

In the library, you learn that you need a Book of Seals to reach the Fairy Powder in the back. You can't access the powder without using the Book of Seals, even if you have read a walkthrough and know the correct path!

The people in the library also speak of a strange creature who appears to the west and doesn't speak but seems to need help. They also mention the Fairy Queen, who used to live on an island to the west but who has recently disappeared.

Get the Book of Seals

Travel to the present. The library in the present time will now be open. Go inside and learn that there is no fairy powder in the back, but there is an old book. You will also learn that the fairy powder can be used to turn the cursed queen back to her original form.

Go outside and go to the past, then walk west of the Library. Use the Switch Hook on the diamond. Go west, then into the cave, and go up and talk to the Octorok.

Go to the back to the Library in the present and talk to the old man in the back to receive the Book of Seals. He will only give it to you if you talked to the Octorok in the cave west of the Library in the past.

Get the Fairy Powder

Go outside and return to the past. Go to the back of the library in the past. Put the book of seals onto the podium.

Read the book and you will see a code. You have to read the book, or there will be no invisible path to walk on! Each book's code is listed below, or you can skip ahead to the Book of Seals Map, but remember that you have to read each book along the path, or the path won't be there.
>4 ^2 >2.
Walk four steps to the right, two steps up, and two to the right. You can create a block with the Cane of Somaria to help you count properly.

You arrive above the book on the right. Read it:
^2 <1 ^2 >1 ^1
Walk two steps up, one step left, two steps up, one step right, and one step up.

Read the book above you:
<2 ^1 <3
Walk two steps left, one step up, and three steps left.

Read the book to your left:
↓1 <3 ^1 <3
Walk down one step, left three steps, up one step, and left three steps.

Read the book to your left:
↓1 >1 ↓2 <2 ↓3
Walk one step down, one step right, two steps down, two steps left, and three steps down.

Read the book below you:
>1 ↓1 >2 ^1 >1 ^1 >2
Walk one step right, one step down, two steps right, one step up, one step right, one step up, and two steps right.

Talk to the old man to get the Fairy Powder.

Book of Seals Map

Below is a map of the path through the Book of Seals room. NOTE: The paths don't exist until you read the books, so be sure to read each one.

Read each book to make the paths exist.
  * * * * * *
 B4444 B3333 B
* 55 4444  332*
   5        22
*555        2 *
 5     F    22
*5   666     2*
 56 66     111
*B666  B   1 B*
       L1111
       |  * *
    Entrance

* = Torch
L = Link's position after reading the Book of Seals
B = A book along the path
F = The old man who awards the Fairy Powder
# = Each number represents the path that you can walk after you read each book

Save the Fairy

Go to the west. In the past, there is a stone diamond on the island to the west of the library. Use the Switch Hook on it to go over to the island. Go inside the cave and give the Fairy Powder to the Octorok. It will turn back into the fairy, who will go around and cleanse the ocean. All of the blobs of poisonous jelly in the ocean are now gone.

Get Permission to Visit Jabu-Jabu's Belly

Talk to King Zora in the present. He will give you permission to go to Jabu-Jabu's belly. Jabu-Jabu is underwater, to the west of the Zora Village throne room in the present. Swim over to Jabu-Jabu and he will open his mouth, allowing you to swim in.