Task 1: To Princess Zelda
Following your success in Lakebed Temple, you are transported to the Lanayru Spirit Spring. The king of the twilight, Zant, comes to meet you and he chides Midna for thinking that the Fused Shadows could stop him. He then uses his powers to embed a crystal in your head, trapping you in wolf form, and to injure Midna.
The Secret Entrance
You have to see Princess Zelda about what just happened, so start by walking to Castle Town. Though the humans are afraid of you, the animals are willing to help. Head into Telma's bar, you'll be kicked out and Telma's cat, Louise, will follow you. She explains that there is a secret entrance into the castle and points you to the opening. Push a nearby box to get enough of a boost to reach it. Once inside the bar, walk across the ropes and listen to the conversation when prompted to. You may move the pots blocking the ropes, but don't let them fall.
After you leave the bar, you'll end up in Jovani's house. He asks you to defeat a poe for him in order to restore part of his soul. Engage your senses and attack the poe (jump attacks are effective) until it falls. When its soul (a blackish orb) appears, target the poe and press to take the soul. After you finish with that, Jovani asks to find 20 souls and he opens the passage to the waterway for you.
Note: Depending if you met them before or not, they'll realize after listening to Telma who you really are. The text will determine what the group thinks of you. Don't be afraid to do this if you like to experiment as there is no rule about doing this in order.
Your journey through the waterway begins at a hub. Walk around the ledge, defeat the rats, then pull a chain. That will open a route to the north. After you float to the castle basement, you'll go up against a pair of skulltula. Burn their web with a flaming stick after you defeat them, and light torches as you proceed onward. Relight the stick on a torch if it goes out, and burn another web. At the dead end, engage your senses to find a digging spot.
Up the Castle
When you emerge, turn left and go up the spiraling staircase, using the ropes to climb upwards. At the top, work your way across the rooftops again. At the part where Midna helped you the last time, there will be a bridge that rises with the wind. Once it is up, jump onto it and work your way across before the wind dies down again. Go across the narrow rooftop to enter Zelda's chamber.
Zelda realizes that you are bound by an evil force. Deaf to Midna's pleas to tell you where the Mirror of Twilight is located, she tells you to go back to Faron Woods and find the sword that rests there to free yourself of the curse. She then sacrifices herself to heal Midna's injuries.
Task 2: Getting the Master Sword
To Sacred Grove
Return to Faron Woods. When you reach the area near the Forest Temple, you'll find a monkey surrounded by strange enemies. You can defeat them with ease, then learn about another section of forest on the other side of a cliff. Climb atop a stump east of the monkey and let Midna guide you to the area on the other side. After Midna leads you across several gaps, you'll fight off a group of Keese. Move onwards to the rotating bridge sections. Get to the next platform beyond the bridges, then cross two ropes while avoiding swinging logs. At the far end, you'll find a howling stone. Match its tune to cause the golden wolf to appear.
Shortly after the howling stone, you'll find yet another…howling stone? When you howl at this one, however, it does not unlock a hidden skill, but triggers the appearance of Skull Kid and his skeletal followers. Defeat the skeletal beings, then follow the leader. As you follow him, he calls up more skeletons. Destroy them and bite their leader when you find him. He opens up a new section of the maze. After a few bites, he'll lead you to an arena. Fight his followers then hit the leader while he is blowing on his instrument. Successful bites cause the Skull Kid to call his henchmen in greater numbers. You'll eventually chase the Skull Kid away and open up a new area.
The Puzzle of the Sword
At the entrance to the Sacred Grove, you'll howl from a symbol on the ground to make two stone giants come to life on a group of blocks. They'll ask you to lead them to their sentry posts by hopping from block to block. Jump in this pattern to lead them correctly: left, down, right, right, up, left, up, up, left, down, down, right, and up.
The next area contains the Master Sword. You walk up to it and it emits a bright light as you touch it. You return to your human form and the Shadow Crystal, the embodiment of the evil magic Zant cast on you, will drop to the ground. Midna explains that the object allows you to turn into a wolf at any time, and if you want to transform or warp, you just need to call her.
Special note: Remember Faron Woods near Forest Temple, Lost Woods and Sacred Grove because you'll be coming back again to access Temple of Time but in human form.