A.N. So things will be done a little differently than from before. Because there are now so many characters, we will have multiple scene switches. It's sort of like how Game of Thrones does things, except George R.R. Martin is a literary genius, and I'm just a fanfiction writer.
As before, I give you the three Rs:
Read
Review
Request songs be put onto the Soundtrack.

Ruto
Two years later, Hyrule.
The entire countryside was in a grumpy sort of mood lately. It had been raining pretty hard throughout the entire kingdom.
The Zora were the only ones not complaining. After all, Should there be a flood, that only meant more room for them to swim.
Of course , being long-time allies to the Hylian Royal Family, they would never voice these thoughts aloud.
As Princess Ruto stared out into the pouring rain, she prayed that her Hero Of Time would come to visit.
Since she had left the Sacred Realm, he had not come to visit her once.
There were troubling rumors about the Crystal Kingdom rising up again. Rumors that the Mushroom Kingdom and Sarasaland had been captured by the Crystal Kingdom had also surfaced, which worried Ruto greatly.
If Peach and Daisy could be taken down so easily, then Zelda was in danger.
She had to get to Zelda before these Crystal Monsters took her too.
With a deep breath, she dove into the icy waters and began to swim for Castle Town.
-

Syrio
"HYAAHHH!YAAAAHHH!" Link yelled as he charged at his sparring partner.
Syrio Toadstool sidestepped and avoided the attack and Link slid on the slippery wet grass and landed on the ground.

"You need to stop screaming before you attack." He commented. "It gives you away. If you do that every time you swing your sword, I'm surprised you defeated Ganondorf."

Link let out an angry noise as he got to his feet.
He didn't need a lecture from HIM of all people. Especially about his fighting choices.

Syrio wagged his finger.
''Anger breeds mistakes. Mistakes breed bad sword fighting. Bad sword fighting breeds a sword to the throat." He intoned seriously. "Remember that. The Sacred Realm's barriers grow weak. Ganondorf will be escaping any day now."
Link clenched his fist. As much as he hated to admit it, Syrio was right.
Ruto had left the Sacred realm. With one Sage gone, the Sacred Realm was not going to hold Ganondorf for very long. He was surprised he hadn't gotten out yet.

"If..he gets out." Link sheathed his sword. "I'll kill him. After all he did to Hyrule, he doesn't deserve life."
It was a rather harsh way to think, but it was GANONDORF after all. He deserved no pity for the atrocities he had committed.
Syrio clenched his fist as he sheathed his sword.
" There are people worse than him." He snapped. "People like the ones who killed my God daughter. Who lulled her into a false sense of security before they threw her to her death. When they come here and try to replace your Queen with one of their generals, you may be happy to have someone like him fighting on the same side as you."
It had been two years and even now, he still had nightmares of that night.
In his nightmares, he saw his beloved Niece assuring him that she would be fine. That she would come home safely with her family.
It had never happened. B.J. had found him on the High Road and told him of his God daughter's death.

Link patted his shoulder hesitantly.
"We all wept when Princess Raven died. She was a kind hearted soul. Kind enough to change Bowser's way of thinking." He hesitated. "I had hoped to be able to meet her one day to test my sword against hers. It never happened. If Ganondorf is released from the Sacred Realm, I'll send him back without a head."

"Let's get out of the rain.'' Syrio muttered.

As so, Link led him to his Cottage near the Lake. He had been here since Ganondorf had been defeated. The Kokori wouldn't accept him in their village anymore. He was pretty sure it was because he didn't look like himself.
"Would you like some tea?" Link offered, filling the kettle with water and placing it on the stove.

Syrio nodded solemnly.
"I need to get an Audience with your Queen. Can you help?"
"Of course.'' Link commented. "She trusts me with her life.. Syrio? Might I ask you something?"
Syrio looked up.
"Yes?"

"Who's your squire?" He gestured to the boy who was unloading Syrio's gear outside in the rain.

"His name is Veren." Syrio called out for the boy to come inside. As the boy shuffled inside, Link could see heavy scarring on his face.

"What happened to this squire to warrant such heavy scars?"
Syrio looked a bit ashamed.
"When we got here, we accidentally angered one of the Garudos that still believed in Ganondorf's cause. They attacked us. We barely escaped with our lives."

-
Zelda
Zelda was entertaining a few guests in her Solar when a giant tremor rocked through her palace.
As she peered out the window, her face went white as a sheet.
There was a rather large airship flying towards them, bearing the flag of the Mushroom Kingdom.
She turned to her guests.
"Please take shelter in the Temple of Time." She requested. "My guards will show you the way there."
As the Guards escorted them, Impa entered the room.
"Impa." Zelda said relieved. "Please help the guards get everyone into the Temple of Time."
Impa turned and began sprinting after the guard.
Another explosion began to rock the Palace.
As a rather large chunk of Ceiling fell towards Zelda, she felt herself being picked up.
As her Solar crumbled, she found herself out in the garden.
"How on Earth-" She began but was interrupted by a familiar voice.
"Princess Zelda."
Eyes widening, she looked up, praying it was not who she thought it was.
Luck was not on her side, however, as Ganondorf stared back down at her.
"Are you alright?"
In an instant, Zelda smacked his hand away and backed up.
"How? Why? How are you-"
Ganondorf chuckled.
"The seal was broken when one sage left. I return to see you in the middle of a battle. Did the Sheikah not teach you to defend yourself?"
Zelda's eyes hardened.
"Temporary truce then?"
Ganondorf held out his hand.
"For now."
Zelda took a deep breath and shook his hand. Then with a toss of a Deku nut, She transformed into Sheik.
"Let's take these fools down."

Thalia

A small group of armed warriors moved through the shadows of the Mushroom Kingdom's Capital, Aurora Capitolis.
They were led by a woman in red armor. Her bright red hair was twisted into a tight braid and her eyes were violet and stern.
As they moved through the city, Toads not turned into Crystal Clones watched in admiration.
It had been years since The King's youngest sister had been seen. Shortly after the six Kingdoms had banded together to banish the Crystal kingdom, she had disappeared without a trace.
Now she had returned to take back her brother's kingdom from the ones she had fought so hard against during the Crystal wars.
Instead of marching right to the castle, she took a detour to Peach's personal assistant's house.
She knocked.
"Toad." She called.
A bleary eyed Toad answered the door.
"Thalia? Jeez, it's been forever. What do you want?" He asked sleepily, not comprehending what was happening.
Thalia raised an eyebrow.
"I need access to your secret entrance to the Castle. We're going to lay siege to it and take it back by force.''
Toad rubbed his eyes.
"Is that really you Thalia?" He asked, a bit nervously. If this was a fake, he could end up getting killed.
Thalia held out her hand. On the hand was engraved a Mushroom with the Triforce upon its face.
The sign of the Rebels.
Toad immediately opened his door the rest of the way.
"Come on in."