Chapter 3: What Is This World?
Sora was spooked out of a sound sleep and jumped out of bed, unfortunately Sora had the top bunk that morning. He fell out of bed after he slammed his head on the ceiling.
"Oww, Donald, what did you do that for?" Sora moaned.
"Look at me!" Donald said.
Sora saw that Donald didn't look like himself. He was a little smaller, his hands looked more so like wings, and he wasn't wearing his wizard's outfit.
"I guess being in this new world must've changed your appearance, like the others."
"I was the one doin' the changing, you big palooka!" Donald yelled.
"Eh, heh-heh, right, I forgot." Sora said while scratching his cheek and grinning sheepishly.
"Well, how come YOU haven't changed?!" Donald yelled.
"I don't know!" Sora said. "Let's do some walking around, we'll figure it out."
"Oh, all right." Donald said.
They opened the loading platform and exited the ship. When they did, Sora looked down at the front of the school, he saw a girl laying on the ground, he started to panic until he saw her move, she was waking up. "Who would fall asleep on the ground? Did the Heartless get here already?" Sora thought to himself. If the Heartless were here, he can't waste any time. Besides, she doesn't look like she had her heart taken. She should be fine. For now. Sora continued over to the staircase that was on the roof. They climbed down the steps and came into a hallway. To Sora, it seemed abandoned because there was no one around, but he knew better than that. Someone had to be here, an entire building can't just be empty (especially one so big and new-looking). Sora and Donald kept walking around, but still found nobody. Was it possible that no one was here? It doesn't make-
BRRRRRRRRRRIING!!!
It was obvious that this place wasn't abandoned. People began to pour out of the doorways, flooding the hall with teenagers. Sora and Donald were struggling to make their way around the others, but to little avail. They stuck it out until the hallway finally calmed down a bit, enough to walk through. He tried talking to the people around the building, asking them if they had seen anything strange lately; they all answered the same thing, "No". Sora and Donald were being to think that the Heartless hadn't shown up yet. At least they could relax for a while, knowing that trouble wasn't around the corner, they could continue their search for the magical disturbance. "Hopefully, we won't have any problems until we find the disturbance." Sora thought to himself.
Then Sora and Donald turned a corner in the hallway and-
"Thought this was over, didn't you?"
There was a girl with pink hair, white tank top, and a green skirt being harassed by a girl with red and yellow hair, black jacket, and an orange skirt, Sora and Donald quickly dove back into the corner, preparing to take action if things got too hairy.
"I... I didn't-"
"You are so pathetic! Don't you see that I rule this place? You'll never hide from me!"
"I... I..."
The pink-haired girl was on the verge to tears until Sora finally stepped in.
"Hey! Leave her alone!" Sora shouted running in between the two, blocking them from each other.
"And just who are YOU?!" the red-yellow haired girl asked, annoyed. "Get outta my way!"
She tried to walk around him, but Sora kept cutting her off, making her frustrated.
"Rgggh! You're really getting on my nerves!" the red-yellow haired girl growled. "You know what? I don't have time for this!"
She started to walk away but stopped to turn to Sora and raise a finger to him, "This isn't over." she continued walking until she was out of sight behind the corner that Sora and Donald came from.
The pink-haired girl was astonished by the spiky-haired boy did, he stood up to her bully. He walked up to her with his hand held out, "Are you ok?" he asked.
She hid herself in her hair for a moment until she looked up at him, a blush was slowly coming onto her cheeks as she reached her hand out to grab his.
When Sora had a grasp of her hand, he pulled her up on her feet. She finally had the courage to speak to him, "I can't believe you did that."
Sora was confused for a moment, "Uh, did what?" he asked.
"What you did before, nobody ever stands up to Sunset Shimmer." the pink-haired girl answered.
"'Sunset Shimmer', so that's who that was." Sora said.
"I can't believe I was saved from her twice in a row." the girl said.
"Twice? Someone else helped you?" Sora asked.
"Yes, she was a new student. Um, did you come here from another school?" the girl asked.
"Ummm..." Sora was trying to think.
Donald elbowed his leg to get his attention, when he looked down, Donald nodded, telling him to play along.
"Yeah, I, uh, I did. I'm Sora." he answered.
"I'm... Fluttershy.
"Uh, sorry, I didn't get that." Sora said.
"It's Fluttershy." she answered again.
"'Fluttershy'? Well it's nice to meet you." Sora said.
Fluttershy's gaze drifted down to the white duck next to Sora.
"OH MY GOODNESS!" Fluttershy said, rushing past Sora. "Who this sweet little guy?"
"That's Donald, my, uh, duck." Sora answered.
"He's almost as cute as Twilight's dog, Spike." Fluttershy said, holding Donald in her arms.
"Twilight?" Sora asked.
"Oh, she's the new student I was talking about." Fluttershy answered.
"Ohh." Sora said.
Fluttershy began to scratch the back of Donald head, causing Donald to close his eyes and shake a flipper he had raised in the air. Sora couldn't help but chuckle at Donald, he was acting more like a dog than a duck.
"How do you do that?" Sora asked.
"Oh, this? It's a little trick I learned, ducks have a certain spot on the backs of their heads that if you scratch, they become very friendly towards you." Fluttershy explained.
Sora wasn't sure how that was possible, but it's a different world, so things tend to be a little, if not a lot, different.
"Attention students, due to a new student at Canterlot High, any and all other new students must report to Principal Celestia's office for orientation. That is all."
Sora, Donald, and Fluttershy heard the announcement, so Fluttershy let go of Donald and stood up.
"You should probably get going." Fluttershy said.
"Yeah. So I'll see you around?" Sora asked.
"Maybe... if that's ok with you, I mean." Fluttershy whispered her answer.
"Ok, bye!" Sora said, running off.
"Oh, wait!" Fluttershy called.
Sora and Donald snapped their heads back to Fluttershy, who had a backpack in her hand.
"You're not really supposed to have pets on school grounds, I have a spare backpack that you can tuck Donald into, I mean, if you want to." Fluttershy explained.
"Thanks Fluttershy." Sora said with a smile as he put on the backpack.
Donald quickly hopped into it and the two ran off into the distance. As Fluttershy watched them leave, she couldn't help but blush at the thought of her savior.
"Oh... M-My..."
To Be Continued...
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I don't want to go all Kingdom Hearts autist here, but this is a common misconception I run into with kingdom hearts crossovers. The transformations that Sora and company undergo in worlds like Atlantica, Halloween Town, and the Pride Lands are not the result of the world's magic. They're the result of Donald's magic actively being used to transform the crew so they'll blend in or survive in a environment they normally wouldn't be able to. While Canterlot High could be a Fisher Kingdom there's no way of telling for sure if it's the world itself that turned spike into a dog and twilight into a human on arrival or if the transformation was a function of the mirror. That said as the writer you do have the power to declare Canterlot High a Fisher Kingdom for the purposes of this story which can work to your favor. Rather than have Donald's transformation be hand waved as something that happens all the time, have him freak out because he has no idea how or why this happened and bam, instant Donald subplot. You would need to have Sora ask something like "what's the big deal we transform all time" so that Donald can explain the fact that he's been behind all their past transformations and he's never seen anything like this in his entire time as King Micky's court wizard. This sets up an Oh shit moment for Sora and helps to ratchet up the tension at the start of the story.
Also I should point out that if the title of the chapter makes no sense. Sora would know what school is. The destiny islands has a whole small town on the main Island complete with a functional high school as evidenced by Kairi and Selphi's school uniforms in Kingdom Hearts 2.
All that said I'm enjoying the story so far; the characterization for Sora and Donald is pretty spot on. Keep it up man. Also if you want an editor / fact checker for the story I'm not doing anything pressing and I'd love to help keep the story consistent with Kingdom Hearts metaphysics and lore which is admittedly incredibly confusing.
Oh, yes, because having a duck at school won't arouse any suspicion (sarcasm duly noted). Having a duck at school. Sounds like the start of a joke.
It probably is! 
I like the idea that you are basically re-inventing the first meetings with the human mane 6 except it is Sora doing the stuff is Sora going to enter the competition for the fall formal crown because that would be cool. I like the hint to a Sora x Fluttershy shipping I look forward to how this will turn out
4728057 something I've noticed in KH stories is they like to pair Sora with Flutershy a lot.
....a blush? Oy vey.
4819858 Sorashy?
5340170 Fluttersky!
4819858 i wonder,what for? cuz she's kinda like Sora,Roxas and Ven?
4819858 why?
Ok so now I see you made Donald look more like a real duck, ok. That is so funny, cool stuff dude like it.
Bringing duck to school! Pewdiepie will be proud !!
Fluttershy like Sora
Fluttershy like Sora
Fluttershy like Sora
All we need is a blue sailor costume.