My Little Layton: Puzzles are Magic

Chapters

a new investigation
friends and foes
entering the catacombs
Iris
Rotten Heart and Discord

a new investigation

Luke and the professor walked through the streets of London. As they walked into the library, they saw a girl with dark hair streaked with pink and purple. When she saw Luke glance over she hid her face behind her book. Luke raised an eyebrow. He nudged the professor in the ribs
“Professor, look at that girl over there.” he told him quietly. The professor glanced over
“Hmm… she certainly is different-looking.” He said “I’m sure she’s here for the same reason we are.”
However, at the café half an hour later, Luke saw the girl again with a girl wearing a yellow dress and light pink hair, and they were looking at the professor and Luke.
“I think we’re being followed.” Luke told the professor quietly
“Perhaps…” agreed Layton. They went back to the professors flat, and Luke saw the two girls meet up with several other girls. The wind carried up snatches of their conversation
“I told ya’ll to be careful!”
“A.J., we’ll handle this!”
“Maybe we should ask someone else…”
“Nonsense, Fluttershy! They’re the only ones who can help!”
“Why not just go up there and explain?”
“We might just have to…”
The next day, Luke saw the dark haired girl again.
“Excuse me?” she asked, going up to him and the professor. “Are you Luke Triton and Professor Layton?”
“Yes.” Said Luke
“I need to show you something. You see, my teacher sent me here with my friends because we have a bit of a problem… and she thinks that only you two can help us.” Said the girl
“Well, a gentleman never ignores the request of a lady.” Said the professor “we’ll try and do what we can.” The girl smiled
“That’s great! I’ll go get my friends!” later, Luke and the professor met the girl and her friends
“Ok, rarity I’ll need your help with this.” Said the dark haired girl
“right.” Said another dark haired girl wearing a white dress. The two girls’ grabbed hands and an aura shone around them. Their eyes shone with a bright light
“Almost…” muttered the girl in the white dress
“Professor, what’s going on?!” asked Luke.
“I don’t know, Luke…!” said the professor. Suddenly, they were transported to a grassy field outside a forest.
“Ugh… I hurt all over…” whined Luke. He looked at his…
“HOOVES?!” he shouted. He looked over his body “wh-wh-why am I a horse?!” he asked
“The term is ‘pony’” said the pony who was the girl in the white dress. She had a horn on her forehead, same with the pony who had the dark hair. The one who had worn the yellow dress was a pony with wings.
“Ah man, it feels so good to be a pony again! I hated being grounded!” said one winged pony who had rainbow colored hair. She did loop-the-loops in the air “I just wanna' race around!”
“Now hang on their sugar cube we gotta' explain!” said a pony with blonde hair who gave off a cowgirl look. She turned to Luke and the professor “mighty sorry. My friend here has been antsy since we went to ya’ll’s world since she wasn’t able to fly.”
“Of… course…” said the professor as he examined his own body.
“Come ooooon! We need to get to Canterlot! They gotta’ meet the PRINCESS! Twilight, rarity, you two messed up on where to SEND US!” said one pony, who had fluffy pink hair and had a pink coat
“She’s right, twilight. We’re supposed to take them to Princess Celestia and Princess Luna for them to explain.” Said the blonde haired pony
“Right. Let’s go gang, and remember what the princess said, no one can know about Luke and the professor.” Said twilight. A little later, they were on a train, in a compartment to themselves
“Phew… okay, nopony saw us…”
“I… I hope spike is doing okay watching our pets.” Said the pink haired pony
“I’m sure he’s doing alright.” Said twilight. She looked at Luke and the professor “now, it’s the princess who’s going to explain why you’re here, but I can explain about where we are. We’re in the land of Equestria, where all the citizens are ponies. There are 3 kinds of ponies, technically four but you’ll learn about that later. Those three kinds of ponies are unicorns, Pegasus, and earth ponies. Earth ponies are stronger and have more stamina, pegasi aren’t as strong, but they’re faster and have much more agility. Unicorns are able to perform magic and can organize their minds much more quickly. You two are unicorns.” Luke and the professor looked at their reflection and saw that they were unicorns. “Hey, neat!” said Luke
“As you heard my names Twilight. My full name is Twilight Sparkle, but you can just call me Twilight. The blonde pony right here is Applejack. The Pegasus with the pink hair is Fluttershy, the rainbow haired one is Rainbow Dash, the white pony is Rarity, and the pink one is Pinkie Pie.”
“Hershel Layton.” Said the professor
“Luke triton.” Said Luke.
When they arrived at the castle’s throne room, two ponies were standing, talking
“Princess! We’re back!” said twilight
“Twilight!” said the taller of the two with rainbow colored hair “welcome home, my dear!” she turned to Luke and the professor “you must be professor Layton and Luke. Welcome to Equestria. I am its princess of the day, Princess Celestia. This pony right here-“ she nodded towards the darker pony beside her “-is my sister Luna, the princess of the night. You’ve already met my student Twilight Sparkle, and her friends. They’ve taught you about Equestria, and now it falls to me to tell you why you’re here.” Celestia’s horn glowed and a book flew off a shelf in front of the professor, who held it up with his own magic “These are Changelings. There a species of creature who disguise themselves as a pony and then gain strength by feeding off your feelings for others. We had problems with them before when they threatened to destroy Canterlot when their queen disguised herself as the princess of a neighboring kingdom to Equestria, Cadence, when she was about to marry Twilights brother, Shining Armor, who is now prince of that kingdom. We thought we had banished them for a long while, but a few have slipped out to Ponyville, and now are trying to gain strength so their queen, Chrysalis, can return. Last time she sought to take over, it was the love of Twilights brother, Shining Armor, and his wife, Princess Cadence, that saved the day when their love gave Shining Armor the strength to cast the spell needed to drive them back. But I’m afraid they’re back again! They’ve too-“
“I'm very sorry to interrupt you, but might I ask...why do you need our service?"” Professor Layton asked.
“Why, they’ve kidnapped my husband, Shining Armor!” a voice said. It was a pony with many colored hair.
“You must be Cadence.” Said Layton
“yes.” Said cadence “As I said, the Changelings have kidnapped my husband, learning from last time. Without him, the spell cannot be cast to drive the Changelings back to where they belong.”
“However, there is a kind of prophecy, which leads to where you and your apprentice come in, Professor.” Said Celestia
“The prophecy recites thus:
When the dark ones rise and the protection has been taken, a portal to another world shall open, and two shall be found who can tell friend from foe. With those of evil found and the protection returned, the evil shall be cast back.” Recited Luna
“And you think we’re the ones mentioned in this prophecy?” asked Luke
“I sent Twilight and her friends through the portal that was mentioned. It was really a spell that took them to your world, where they found you.”
“I knew that we’d need to search for someone clever, and you came up many times in newspapers, Professor. We watched you for a couple of days, until finally we were sure that you and Luke were the ones we needed.” Said Twilight
“I understand you’re confused and might not want to help, but Equestria could be in terrible danger if the Changelings aren’t stopped. Please, Hershel Layton, will you help us? Will you help Twilight determine Pony from Changeling as they work to free Shining Armor?” asked Celestia
“Well, I for one won’t say no!” said Luke immidiently, stamping his hoof “whether or not the professor decides to stay, I’m staying myself! I can’t go back home knowing this world might be in trouble if I can do something about it!”
“Well, I can’t very well go home if Luke is staying. People would notice if he disappeared, and it’s my job as his temporary garden and his father’s friend to look after him.” Said the professor “Besides, no gentleman could ignore a request from a lady, especially a princess.”
“Thank you. Twilight and her friends will escort you to Ponyville in the morning, but right now it’s getting late and you’re probably very tired. Twilight, could you show our guests to the rooms in the east tower?”
“Right away, princess!” said Twilight. She showed Luke and the professor to their room “Here you go!” she said “My friends and I will be down the hall. Turn left at the end of the hallway and we’re three doors down on the left. Just come by if you need anything. Good night, Luke, Professor.”
“Twilight, wait! I have one more question.” Said Luke
“Your just full of them, huh Luke?” laughed twilight “Rarity told me more than once that me and you were alike in a lot of ways. What is it?”
“Well, I noticed that a lot of ponies have symbols on their flanks. Why?”
“Their called cutie marks. You see Luke, when a filly or colt reaches a certain age and discovers his or her certain talent; a mark appears on their flank that shows it. It can represent their talent as well as an aspect of their personality. When your younger, it’s always fun guessing what your cutie mark might be. There are 3 foals in Ponyville who are around your age who are what are known as blank flanks, meaning that they don’t have their marks yet. They formed a group called the cutie mark crusaders.” Twilight chuckled “their names are Applebloom, Sweetiebell, and Scootaloo. Applebloom and Sweetiebell are Applejack and Rarity’s sisters, and Scootaloo and Rainbow Dash are like sisters.” Luke looked down at his flank, but saw nothing
“I don’t have my mark…” he said sadly “I wonder why?” he went over to the professor, and saw a picture of his wax seal “aw man…”
“Ah, don’t fret my boy! I’m sure you’ll have your mark by the time we return home.” Said the professor
“I hope so… it’s really disappointing that I don’t have it yet…”
“Well, that’s 3 friends you’ll have in Ponyville. The crusaders are always on the lookout for foals their own age that don’t have their marks.” Said Twilight. She sighed “it’s a shame. A foal is supposed to earn his or her mark on their own, and we know just what the crusaders should do. We can’t help them because like I said, they need to figure it out for themselves.”
“What do you think their talents should be?” asked Luke as he climbed onto his bed
“Well, Sweetiebell is a great singer, but she’s so shy about it. Applebloom can repair a home like no one’s business, she even built the crusaders clubhouse, and Scootaloo does great on her scooter.” Said twilight “but don’t worry Luke, I’m positive you’ll get your mark. Like I told you earlier, my friends and I had been watching you and the professor! We know you’re great at puzzles, which reminds me, I thought one up earlier and thought you might like to hear it.”
“Sure!” said Luke, perking up
“Alright.” Said Twilight. She cleared her throat “Four stallions go to sit by each other. You don’t know their names, but each one has a different colored coat. One is red, one is blue, one is yellow, and one is green. With only these two pieces of knowledge, figure out how the four will sit in order. The first rule is that the yellow pony is sitting to the left of the red one. The red and blue ponies fight a lot if they sit by each other, so they sit as far from each other as possible. How will they be sitting?”
“Easy! In order, it’s blue, green, yellow, and red!” said Luke, smiling
“That’s right!” said Twilight “Well, I’ll let you two rest. If you need anything, you know where to find us. Good night.” And she left the room. Luke and the professor turned out the light. Luke yawned
“This has been interesting day, huh professor?” he asked
“It certainly has, my boy.” Said the professor as his horn glowed as he magicked off his and Luke's hats
“You think Flora will be okay?” asked Luke “I’m kind of worried…”
“She can handle herself one night. Tomorrow we’ll ask Twilight and her friends to try and bring her here.” Said the professor “Try and rest Luke.”
“Yes, professor.” Yawned Luke “good night.”
“Good night, my boy.” Said the professor. The two quickly fell asleep, or at least…for a while.
Creeeeeak
“W-What was that?” Luke said, suddenly awake by the sound. “P-Professor, is that you?”
“Oh, sorry Luke. It was just me.” Professor Layton replied.
“Oh… alright. Sorry, professor.” Said Luke
“It’s alright, Luke. Go on back to bed.” said the professor. As Luke snuggled back under the covers, starting to fall asleep again, he had the strange feeling of something not being right…but, he just couldn’t figure out what.
‘Stop being so afraid Luke. It’s just Professor.’ Luke thought to himself, and with that, he went back to sleep.

Author's Note

in the starting chapter to the colab crossover fic written by me and my buddy peachsapling on deviantart, we have the gentlemanly professor of archaeology, hershel layton, and his apprentice number 1, luke triton, entering the world of equestria and discovering their goal: to help twilight determine pony from changeling so that they can rescue shining armor and drive the changelings back underground where they belong
any part where the fandom seems wrong was written by peach. shes still learning. XD in all seriousness though, she didnt do half bad. I ONLY HAD TO HELP HER OUT A FEW TIMES! lol. peach knows i play~

friends and foes

The next morning dawned bright and early. Luke awoke with a soft snore and a deep yawn “Ahh… morning, professor…” he mumbled “how’d you sleep…?” he asked tiredly.
“Good, good, and how was yours?” Layton replied.
“It was fine. Except…when there was a creaking noise. It was just you though, so it was all good.” Luke said with a smile. “Although…why were you up so late Professor?” Luke asked.
“I was up late at night? I…I don’t recall getting up late at night. Strange…” Layton said as he magicked out his journal. “Interesting…Luke, what happened when this happened?” Layton asked.
“Well, I just asked who was there, and you answered that it was you. You told me to go on back to bed, so I did. Now that I think about it though, I had been pretty tired. It might have just been a dream.” Said Luke as he got out of bed. He went to reach for his cap, but paused. He smiled and closed his eyes, concentrating hard. He levitated his cap off the table and on to his head “Haha! Yes! I did it!” he cheered, laughing.
“Good job, my boy. You’re learning quickly.” Said Hershel as he levitated his own cap “well, I suppose first we should go see Twilight and perhaps our two hosts, princess Celestia and Princess Luna.”
“Right!” said Luke “this is going to be one interesting investigation, if we can even call it that.”
“Well my boy, we’d better get going!” Layton exclaimed. And so, the two of them walked out of the room. As they walked down the hallway they spotted Twilight
“Morning Twilight.” Said Luke
“Morning! We leave for Ponyville in about an hour. We have enough time for breakfast before we have to go catch our train.” Said Twilight
“Not with Luke.” Said Layton, chuckling
“What? I’m a growing boy with a big appetite!” laughed Luke
“That, my dear boy, is an understatement.” Said Layton, shaking his head with a smile
“I wouldn’t be surprised if your Cutie Mark is a plate of food, hearing what’s going on.” Twilight added in with a chuckle. “I know a great place called Sugar Cube Corner, it’s in Ponyville!”
“DID I HEAR SUGAR CUBE CORNER?!” cheered Pinkie Pie, bouncing around the corner “It’d be a great place to take Luke and the prof!”
“Sugar Cube Corner? Even the name sounds tasty!” said Luke, his mouth watering
“It’s where I work! It’s run by Mr. and Mrs. Cake. It’s the town bakery and sweet shop!” said Pinkie Pie
“Professor, can we please go?!” asked Luke “please!”
“Well…” said the professor, thinking
“Pleeeeeeease!” begged Luke. Layton laughed
“Alright my boy, I suppose so.”
“Yes! Thanks, professor!” cheered Luke
“Come along! This way! To the train station!” Pinkie Pie exclaimed as she bounded her way to the Train Station.
“Hmm, it appears as if the train is late.” Twilight said as she checked the times.
“I believe you are mistaken. It just didn’t reach its intended destination in a timely manner. Even trains make mistakes!” Layton added on. Almost on cue, the train arrived. And so, the four of them went off the train to Ponyville.
-ONE TRAIN RIDE LATER-
“Here we are!” said Twilight as they arrived. “Now, before we settle you guys in here in town, let me give you the grand tour.” And she led Luke and the professor through the town.
“Up there-“ she said, pointing to a large house up in Ponyville’s low clouds where a beautiful house was “-is rainbows house.”
“Is it made of… clouds?!” asked Luke
“Yup! Lots of Pegasi have their houses made of clouds, especially since a lot of Pegasi live in Cloudsdale, which is the Pegasi city in the clouds.” Said Rainbow Dash, flying up ahead
“Cool!” said Luke
“Towards the edge of town is my cottage. Which reminds me, I hope you don’t mind if I leave? I’d like to join you, but Angel is probably very upset because I was gone.” Said Fluttershy
“Of course not. But, who is Angel?” asked the professor
“Oh, Angel is my pet bunny rabbit. She’s such a sweetie, but she gets very grumpy without me around.” Said Fluttershy
“Spike should be watching them at my house. You can go and get Angel, Fluttershy.” Said Twilight
“Oh, thank you so much, Twilight.” Said Fluttershy. She walked towards Twilight’s house to get her rabbit.
“Now, we’ll stop at my place last, since you two will be staying my guest room. Our next stop is the market, where we have rarity’s boutique-“
Rarity gasped “MY WORD! I just remembered! I have a dress to finish for a very important client, and she’s coming tomorrow! Sorry girls, but I simply must run!” she said
“Well, we’ll stop by the boutique first.” Said Twilight, and they walked towards Boutique Carousel. Rarity magicked open the door quickly, and they continued onward.
“Next stop is Sugar Cube Corner!” Twilight said with glee, followed by a whoop of joy from Pinkie Pie and Luke. When they arrived, pinkie bounced in “Mr. and Mrs. Cake! I’m back!” she said
“Oh, Pinkie, we’re so glad your back! We have a big order that needs to be filled, and could really use your help!” said Mrs. Cake
“I’ll get the sugar and-“ started Pinkie
“No, pinkie, we need you to watch the twins.” Said Mr. Cake
“Oh, sure thing! Are they upstairs in the nursery?” asked Pinkie Pie
“Yes, dear. They just had their snack. Could you be a dear and put them to bed, please?” asked Mrs. Cake
“Sure thing!” said pinkie. They went upstairs where the twins were playing.
“Okay little ones, it’s time for your nappy!” said Pinkie Pie “so be good babies for aunty Pinkie!” she said as she put them in their cribs. They whined a bit “Aww! It’s okay kiddies, we’ll play later, I promise!” said pinkie pie “now go on to bed now.” And they all went back down stairs
“I reckon we should check on the fillies. Who knows what trouble they got in to while we were gone?” said Applejack. When they arrived at the farm, Applebloom was bucking trees to get apples for her and her friends
“Hey, Rainbow Dash! Ready to start our flying lessons today?” asked one of them, who had an orange coat and fuchsia hair
“Sorry Scoot, can’t right now. Maybe later, alright?” said Rainbow Dash
“Aww… ok…” said Scootaloo. She saw Luke who was just around their own age and gasped when she saw he didn’t have his mark “GIRLS! HE’S A BLANK FLANK!” the two other girls, one with a white coat and lavender hair and one with a yellow coat and bright red hair rushed over to Luke and started questioning him at super-fast speed
“What’s your name?” asked the one with red hair
“Where’d you come from?” asked Scootaloo
“I really like your mane!” said the one with lavender hair
“Ummm… uh…” stuttered Luke
“Girls! Girls!” said Applejack “Leave him alone!” she said “He just got into town! What did we tell ya’ll fillies about pestering new foals that don’t have their marks? Besides, Luke’s only visitin’. He won’t be in town any more than a few weeks.”
“So?” said the girl with bright red hair “Babs started a branch of the Cutie Mark Crusaders in Manehatten!”
“Luke’s from really far away, Applebloom. They don’t worry about cutie marks where he comes from.” Said Applejack. “Now you fillies apologize for pestering him.”
“Sorry…” said the three girls
“Its… it’s alright.” Said Luke
“Applebloom, did ya’ finish your chores?” asked Applejack
“I sure did!” said Applebloom
“Chickens are in the coop?”
“Yup.”
“Apples are bucked?”
“Yup.”
“Kitchens’ clean?”
“Yup.”
“I can check?”
“Uhh…”
“Didn’t think so. Go do your chores, Applebloom.”
“Fine…” mumbled Applebloom. “Come on girls…” and Applebloom and her friends walked off
“I swear, those fillies are a handful.” Sighed Applejack
“They were certainly… friendly.” Said Luke
“They’re the only ones in their class who don’t have their cutie marks. Mine and Applebloom’s cousin in the town of Manehatten, Babs Seed, doesn’t have her mark and started her own Cutie Mark Crusader group there. They’re always excited to make friends with foals who don’t have their cutie marks.” Said Applejack
“Let’s get back to the Sugar Cube Corner shall we?” Twilight said.
“I think I need to watch Applebloom do her chores. Who knows what she’s going to do.” Applejack said as she walked into the house. And so, the group backtracked to Sugar Cube Corner once again.
“Look at these cupcakes, professor!” said Luke, his mouth watering
“Luke, we haven’t even had lunch yet.” Laughed the professor “but I promise, I’ll get you one later.”
“Okay…” said Luke. When they went out to the marketplace to get to Twilights home, Luke saw a Pegasus with curly brown hair and a cutie mark that was the image of a golden-colored apple
“Flora!” said Luke, rushing over
“Luke!” said Flora. The two hugged
“It’s so good to see you!” they told each other
“Professor! It’s so good to see you too!” said Flora, noticing the professor
“Good to see you too, my dear.” Said the professor, looking at Flora.
“Oh, Flora, this is Twilight, Rainbow Dash, and Pinkie Pie.” Said Luke
“It’s a pleasure to meet you all.” Said Flora, smiling.
“Nice to meet you too.” Said Twilight
“Hey there!” said Pinkie Pie
“What’s up?” said Rainbow Dash
“Come on, I know a good café nearby where we can get some lunch.” Said Twilight
“Oh, I’m not really hungry…” said Flora
“I’ll show you to where we’re staying.” Said the professor. As he led Flora to Twilights home in the library, she turned down another street
“Flora, dear, it’s this way.” Said the professor
“I saw something down this way. I want to check it out.” Said Flora. When the professor followed, the sound of insect wings filled the air
“Flora…” said the professor. Suddenly, changelings burst out from the shadows. The professor narrowed his eyes “I had a feeling… where’s the real Flora, imposter?”
“You’ll sssssssee sssssoon enough!” hissed one changeling as the others chuckled. Suddenly, everything went dark. The professor woke up on a stone floor with a splitting headache. “Wh-Where am I…?” he said as he got up
“Why, the crystal catacombs beneath Canterlot.” A voice said. There was a changeling who, in a way, looked like Celestia. “By now my minions have already tricked that naïve ‘apprentice’ of yours.”
“you must be the changeling queen.” Said the professor.
“you’re not as dumb as you look, Mr. Layton! Give up on getting out though, barely anyone even knows these caverns exist.”
“I’ll find a way out, or Luke will find me.” Said the professor
“you’re as naïve as that adorable little friend of yours, professor! Who knows, maybe when I take over, I’ll keep him as a pet!” laughed Chrysalis
“Hurt him, and I won’t hesitate to hurt you.” Said the professor, his horn glowing
“Oh please. You can’t hope to stand up to me! Enjoy your time here, Hershel Layton. You’ll be here for a while.” And chrysalis vanished. The professor’s eyes narrowed.
“Hello?” called a man’s voice “Who’s there?” the professor turned towards the voice as a white stallion with blue hair walked in. When he spotted the professors hat, his eyes widened “You must be professor Layton!”
“I am. And who are you?” asked the professor
“I’m Shining Armor!” said the stallion. “Hang on, wait right here.” He walked around a corner in the cavern and said “It’s okay! It’s him!” the professor heard a girl gasp, and the real Flora ran around the corner
“Professor!” she cried, hugging him “Oh, thank heavens!”
“Flora, dear! Are you alright?” asked the professor, putting a hoof around her shoulder
“As alright as I can be. When you and Luke never came home last night I went out to search for you when these people came and grabbed me! I woke up here as a pony. Mr. shining here has explained everything about where we are and what’s going on.” Said Flora “Professor, where’s Luke? Is he alright?”
“oh no… Luke…! The changelings ambushed me, and their queen said by now they’ve tricked Luke… one changeling disguised itself as you, and they’ve no doubt already done the same with me.” Said the professor
“this means we need to find a way out even more now! Luke could be danger, professor!” said Flora
“I know, my dear.”
“when Chrysalis disguised herself as Cadence, she and Twilight used a mining tunnel to make it back to the surface to stop Chrysalis in time. There has to be something like that around here somewhere.” Said Shining Armor “If we don’t make it back soon, we’ll be too late to stop the changelings before I can get to Cadence. Without her, I can’t cast a strong enough spell to drive all the changelings back.” He looked at the professor “Professor, I have to know; How’s my sister?”
“Twilights just fine. Cadence is as well.” Shining armor sighed with relief
“That’s good. It was only because of her intuition about Cadence that we stopped Chrysalis the last time.” He said
“I just hope Luke is okay…” said Flora “I don’t want anything bad to happen to him!”
“Flora, I told you, you can’t show your feelings for those you care about. Changelings feed off your feelings for others.” Said Shining Armor
“I know, but I can’t help it…” said Flora
“First things first, we need to find a way out.” Said Shining Armor “Twilight and Cadence followed an abandoned mineshaft to just outside the castle.”
“Chrysalis has sealed it up by now, I’m sure.” Said the professor
“Maybe, but it’s our best lead.” Said Shining Armor. “let’s try searching around and seeing if we can’t find anything.” The three got to work on finding a way out
Meanwhile, Luke and Twilight had just arrived home. “Professor, we’re here!” called Luke
“hi Luke!” called the changeling Flora “How was lunch?”
“this kid ran me 30 bits for lunch. I can see what you meant earlier, professor.” Said Twilight
“Totally worth it.” Sighed Luke happily as he sat down “I’ve never exactly been a vegetarian, but I think being turned into a pony helped.”
“I would expect so.” Said the changeling professor. Twilight was searching her desks “Spike! Where’s that book on changelings I asked you to pull for me?” Twilight called up the stairs.
“I’m trying to find it!” Spike replied. “It’s almost like it disappeared off the shelf!” Spike exclaimed.
“Maybe I accidently left it in the bedside drawer! We need this book!” Twilight replied.
“It’s not like it’s been stolen or anything! Professor and I have been in the house all day!” Changeling Flora exclaimed.
‘Hmm…’ thought Luke, getting suspicious “All day, huh?” he asked
“Mhm.” Said the changeling Flora.
“Say, Flora, remind me because this was a couple of years ago, why didn’t you take that money from St. Mystere again?”
“well, because I didn’t want it…” said Flora. Luke frowned
“Not completely.” He said
“Well…”
“and what was the big secret of St. Mystere, again?” he asked
“Well…”
“and remind me of this Flora, what was the Golden Apple?” asked Luke “or maybe I should just call you, changeling!” the changeling Flora frowned and turned back to normal
“You’re not assss dumb as you look!” the changeling hissed “You’re too late though! Your little girlfriend issss ssssomewhere you’ll never find her!” and it fled.
“These changelings are everywhere, I’m telling you Luke.” Changeling Layton said to Luke.
“Yes, but how didn’t you see that that wasn’t the real Flora?” said Luke, turning to the changeling professor, raising an eyebrow
“Now Luke, you’re just getting ridiculous.” Said the changeling professor.
“I…I suppose so.” Luke replied. ‘I have a feeling Flora wasn’t the only one changed…’ Luke thought to himself.

Author's Note

chapter 2! lots of suspense in this chapter when luke finds flora, but it turns out to be a changeling. will he discover that the professor is also now a changeling? he certainly has his suspicions...

entering the catacombs

“Did you send out the letter yet?” Luke asked to Twilight.
“Yep! I sent it to Celestia, and they’ll be on their way to the caverns.” Twilight replied.
“I think we should get going to the cavern under Canterlot.” Discord suggested.
“Alright team, is everyone ready?” Twilight asked.
“Ready!” Everyone but Luke replied.
“Wait! I need my bag!” Luke said as he dashed out of the room and to the guest bedroom. He looked around, and eventually, found his bag on the floor. But, there was something missing…
“Oh no! I lost my teddy bear!” Luke said. He heard someone laugh and Luke blushed
“now, discord! That isn’t very nice!” said Fluttershy. She flew up “do you know where you might have lost it, Luke?” she asked.
“I-I thought it was in my bag…” Luke said shyly, hearing Discord laughing in the background.
“Hmm…well, maybe it fell out.” Fluttershy replied. She then looked under the bed. “Nope, not under here.”
“Is this the teddy bear you’re looking for?” Pinkie Pie said as she came into the room holding the bear. “I found it in Professor Layton’s room!”
“The Professor’s room? I wonder what it was doing in there. I mean, I know he doesn’t mind me having it, it’s just odd that it would be there in all places.” Luke said as he magicked out his notepad and began to write.
“Hey Luke, there’s some sort of…golden hat shaped thing on this bear’s ribbon. Was that there before?” Applejack said as she looked at the bear.
“A gold hat? I don’t think so…” Luke said as he magicked the bear in the air in front of him. There was indeed, a flat, golden hat on the bear. “P-Professor’s hat? And…and there’s writing on the back!”
“Oooh! There’s some writing? Maybe…it’s a secret message! Read it! Read it!” Pinkie Pie exclaimed with glee.
“To Luke, as a reminder to all of the great times we’ve had, I’ve taken the effort to make this little tag for your bear. That way, you’ll always have a piece of me with you. Keep doing what you do my boy, I’m proud of you. –Hershel Layton” Luke read aloud. “Thanks Professor. I’ll always have a piece of you with me!” Luke said as he put the bear back into the bag.
“Alright, now that everyone is ready, let’s go to the cavern!” Twilight said to everyone. And so, they headed off to the cave.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
“So this is the way out?” Flora asked to Rotten Heart, looking into a small tunnel.
“I…I think so.” Rotten Heart replied. “Although, I’m not really sure to be honest with you. It’s just been rumors I’ve heard.”
“Well, it doesn’t hurt to try! …Err, I hope.” Flora said nervously. “If it leads outside, I don’t mind!” Flora said as she started to go into the tunnel.
“Wait, I’ll go with you! L-Like I said, I don’t want you to get hurt!” Rotten Heart said as he followed her.
“You remind me a lot like Luke, Rotten Heart.” Flora said with a giggle. “He’s always protective of me.” Rotten heart blushed slightly
“also, I don’t think it would be wise. What if the professor or shining armor find out about you? If they find out I know about the passage because of a changeling, they’ll get suspicious and there goes our only way out.” Said flora
“I suppose…” said rotten heart “but, don’t forget your promise to me!”
“I won’t. A true lady never goes back on her word.” Said flora
“alright. I’ll try and meet up with you once you’re on the surface.” Said rotten heart. Flora nodded
“agreed. Now, get going! I need to get the professor and shining armor so we can leave.” She said
“what if your friends come while you’re gone? Even if I tell them the truth, how will they know they can trust me?” asked rotting heart. Flora thought
“umm…” she wondered aloud “tell him… tell him that this place reminds me of Folsense. He’ll understand. If you can get that to him, that should at least get his attention.” Said flora. Rotting heart nodded
“alright. be careful, flora. I’ll see you soon.” He said
“you be careful too.” Said flora “now get going!” rotting heart left and flora went to where the professor and shining armor were
“professor! Shining armor! I found a way out!” she said excitedly.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
“Cadence!” Twilight said as she ran to her.
“Twilight!” Cadence replied as they ran towards each other.
“Sunshine, sunshine, ladybugs awake! Clap your hooves and do a little shake!” The two of them said in unison.
“It appears we have found out where the changelings have taken them. A little changeling friend of ours told us.” Discord said with a smirk. “He was very good at pretending to be the Professor.”
“He’s told us that they’re in the Crystal Catacombs, you remember that place?” Twilight asked
“how could I not? I spent weeks trapped in there thanks to chrysalis!” said cadence “should have guessed that chrysalis would keep them there…”
“you coming with us to rescue them?” asked rainbow dash
“of course!” said cadence “with my love spells, I can lead us straight to shining armor, and no doubt the professor is nearby as well.”
“let’s hope.” Said twilight
‘we’re on our way professor…’ thought Luke. When the group arrived at the entrance, cadence led the way. Luke, rarity, and twilight all had their horns aglow to light the way.
“this place gives me the creeps…” said Luke
“Ick! Gross! What did I just step in?!” whined rarity
“rarity, quit whinin’!” said applejack
“I was not whining!” said rarity. “thiiiis is whiiining!” she whined loudly. Everyone chuckled. As Luke looked around, following the others, he spotted rotting heart watching them
“changeling!” he said, everyone immediately turned to it
“wait! I’m not going to hurt you, I promise!” said rotting heart
“like we’d trust you, a changeling!” said cadence
“don’t hurt me, please!” said rotting heart. He looked at Luke, a pleading look in his eyes “I met flora. I didn’t hurt her, I promise. But you all have to leave. M- chrysalis has set up traps for you all!”
“traps or not, we’re not leaving without our friends!” said Luke
“I already showed flora the way out, I promise! She’s just fine, same with Shining Armor and the Professor.” Said rotting heart, backing up, scared “please, you have to believe me!”
“if you’ve met flora, prove it!” said Luke
“she said…. I asked her if there was something I should say to prove that I at least met her. She said to say that this place reminded her of Folsense…” said Rotting Heart. Luke raised an eyebrow
“should we hear what he has to say?” asked discord
“I guess. There are only 3 people in this world who know what Folsense is. Me, flora, and the professor.” Said Luke
“Well then changeling, tell us your queen’s plan!” Twilight said to Rotten Heart.
“I have to? Alright then.” Rotten Heart said as he looked at Luke. “The Queen is planning to separate you from the others one by one and capture them. Then, when it’s just you… she’s going to have you brainwashed, and make you… make you…” rotting heart paused and shook his head “I… I can’t…”
“Oh lord… please don’t tell me. I think I know what you’re saying…” Luke said to Rotten Heart.
“good. Because I really don’t want to say it… but you all need to get out of here, before other changelings show up. If they find out you’re here, we’ll all be in trouble. I showed flora the way out. She’s probably already shown shining armor and the professor out already.” Said rotten heart, looking around “but please, you have to leave right away! There could be other changelings coming here any minute!” just then, the sound of insect wings filled the air and changelings, hissing, ambushed the group.
“Excellent work, rotten heart.” Said a voice as chrysalis came from the shadows.
“chrysalis!” said cadence
“well, hello again cadence.” Said chrysalis, smirking “I’m glad you all have my son, rotten heart.”
“SON?!” they all shouted.

Author's Note

ROTTEN HEART IS THE CHANGELING PRINCE?! DUN DUN DUUUUUN! THISWASTOTALLYUNEXPECTED!!!! pfffft! yeah right! i totally bet you guys expected it. anyway yeah, getting to the climax here.

Iris

“you’re the prince?!” said Luke “to think we almost trusted you!”
“no, I was telling the truth!” said rotten heart
“take rotten heart away from here.” Said chrysalis. “his job is done.”
“no!” said rotten heart as he was led away. He tried to fight them, but they kept getting him back. Rotten heart jumped over the guards, his wings spread wide. He ran towards the entrance to the surface
“after him!” said chrysalis. Changelings rushed after him, but rotten heart was able to evade them. He found flora leading the professor and shining armor out of the passageway
“flora!” he called
“rotten heart!” called flora
“it’s Luke and the others, they were ambushed at the entrance to the catacombs!”
“oh no!” said flora “quick, show me the way!” and flora raced after him
“flora, wait!” called the professor
“no time, professor!” flora called back. “go on! I’ll be okay! Just trust me!” when they arrived at the main entrance to the catacombs, the changelings had the group surrounded. Flora spread her wings and glided over the changelings “Luke!” she called
“flora?!” said Luke as flora landed by him. Flora faced chrysalis “get away from him, you witch!”
“how adorable! The little girl comes to the rescue!” laughed chrysalis
“I know what you had planned, and I’m not letting you hurt anyone!” said flora
“flora, just get out of here!” said Luke
“no way!” said flora
“your quite brave, little girl.” Said chrysalis “my changelings told me you were quite scared when they captured you.”
“I’m brave when I need to help my friends.” Said flora, but she looked around at the changelings surrounding them
“well, let’s see how brave you can be when it’s your friends whom your fighting.” Said chrysalis. Her horn glowed dark green and Luke gasped as his head suddenly felt ready to be torn apart. “Agh…” he muttered “what… what’s going on?!”
“no!” gasped flora “fight it, Luke!”
“I… c-cant…” muttered Luke. Chrysalis smiled evilly.
“Luke!” shouted the professor as he and shining armor rushed in
“professor, he’s being brainwashed!” said flora as twilight and cadence tried to help Luke.
“Luke! Can you hear me?” asked Layton as he turned to Luke
“p-professor, take flora and run!” muttered Luke
“no, we’re not leaving you!” said flora
“go!” said Luke. He let out a shout “just go!”
“but…” said flora quietly, crying
“I’m sorry flora, but I can’t… Agh… fight her off much longer…” said Luke “but I’ll always be your friend… right?”
“right…” replied flora, sniffing
“Friend…friend…” Professor Layton said, as he thought for a moment.
“Professor Layton! Now isn’t the time to think deeply!” Shining Armor said to Layton.
“I’ve got the answer!” Layton exclaimed. “It may just work…it just may.”
“What is it Professor, tell me!” Flora exclaimed.
“I remember…I put a gold chain shaped like a hat on Luke’s bear. If we can read what’s on it, it just might make Luke to his former self again.” Professor Layton explained.
“But Professor…where is his bear?” Flora asked worryingly.
“…In his bag.” Professor Layton said grimly. “And I’m not sure if we can get to it…”
Suddenly, Luke growled and his horn glowed
“perfect!” cheered chrysalis. Luke turned to the professor, a dark look in his eyes.
“Luke…?” he asked
“don’t waste your breath, professor. Your former apprentice is now all mine!” laughed chrysalis darkly as twilight and cadence panted, ready to faint
“cadence! Twili!” said shining armor
“we… we couldn’t do it…” panted cadence. Luke fired out a blast of magic at the professor, who quickly dodged it
“Luke, no!” cried flora “please, snap out of it!”
“Luke, please!” said the professor. Chrysalis watched on, smiling evilly “say goodnight, professor Layton. Your mystery solving days are over. Actually, your days in general are over!” she said, laughing. Luke walked towards the professor, who had been cornered by changelings
“Luke, stop! you’re the professor’s apprentice, remember?!” cried flora “you’re his apprentice number one!” Luke paused for a second, a memory flashing through his mind
“you better get used to it Luke, if you want to be the professors hehe second assistant!”
“I am NOT his second assistant! I am his apprentice, and I am his apprentice number 1!”
He’s stopped! Thought flora “please Luke, just try to remember!”
“remember… that’s it!” said twilight suddenly. She quickly whispered something in fluttershy's ear. She went over said quietly to him “umm… Luke… is it okay if I hold you down against your will for a second?” rainbow dash groaned and quickly flew over to Luke pinning him down changelings hissed and went to attack twilight and the others, but shining armor cast a small protection spell. Twilight went over to Luke, her horn glowing as she cast a memory spell. However, it didn’t seem to work on Luke completely.
“why didn’t it work?” asked twilight “it worked all the other times I did it, back when the girls were turned the opposite of their elements…”
chrysalis laughed “silly unicorn! My spell on the boy is too powerful to be broken by a mere memory spell!” her horn glowed again and shining armors barrier was broken “for the record, I could have done that at any time. I just wanted to see you fail.” She said
“no…” said flora as changelings surrounded them again. Tears fell from her eyes as she looked at Luke, remembering the last time they had spoken back in London
“I’m just so nervous…”
“it’ll be alright flora! No one can match your singing! You’ll sweep the competition!”
“thanks Luke!”
“say, I never actually heard the song you’re singing.”
“I thought I sang it for you already? Well, the professor won’t be back from teaching for a bit. I suppose we have a bit of time...”
“from the first time that I saw you, across the floor, your gold hair in the moonlight, as bright as the sun… you would tell me I’m special, and how my cheeks would glow! I felt just like a princess, that made you my prince…” she sang softly. Everyone turned to look at her, even Luke paused and looked
“you took my hand and I touched your cheek… your eyes, your smile… so sweet to me… I felt so warm, although it was cold… I just need your presence in my life…” flora continued to sing. Twilight and cadence looked at each other, and nodded. Cadence took a deep breath and her horn glowed it’s soft pink. Twilight’s horn glowed it’s standard purple, but suddenly her eyes glowed a soft red as she cast the memory spell again. Luke gasped and shook his head
“wha… what’s going on?” he asked.
“Luke, are you alright?” asked the professor
“yeah…” he said as he shakily got up. Twilight let out a pant as she finished the spell.
“take that!” she taunted to chrysalis “too powerful for a memory spell, huh?!”
chrysalis growled “get them!” she ordered. The changelings attacked
“are you sure your alright, Luke?” asked flora, going over
“I’m fine.” Said Luke. “but I want to show her what happens when you mess with my head and turn me against the professor and my friends!” he let out a magic blast and knocked back several changelings “and that’s just what I’m going to do!”
“We’ll help you Luke, we’ve had past problems with these guys before…” Twilight said.
“Yeah, BIG problems.” Shining Armor added on.
“Add one Professor, and Luke my boy, you’ve got a team.” Professor said with a smile. “Flora, stay back. I don’t want you to get tied into this.”
“Alright Professor…I understand.” Flora said to him.
“Alright, now that we have a proper team, LET’S CHARGE!” Shining Amor shouted. And so, the war had begun! Twilight and her friends worked together to destroy groups of Changelings, and Professor and Luke as well. But the main blow was from Shining Armor and Cadence, who took out half of the entire army. After 15 minutes and the dust settled, there were only a couple of Changelings left, who started to flee.
“You fools! Fleeing from the scene like that. Very well, if my Changelings can’t get you, then I will myself!” Chrysalis said to them.
“go ahead and try.” Said cadence, her horn glowing. Chrysalis’s horn glowed dark green as the two circled each other. Everyone there watched as the young alicorn faced the age-old changeling queen. They fought, dodging and firing blasts of magic. Suddenly there was a bright flash of light and Celestia and Luna appeared, flying down
“princess!” said twilight
“Celestia. Come to save the day, have you?” asked chrysalis, her wings buzzing
“in a manner of speaking.” Said Celestia “I discovered a couple of rather… interesting pieces of information.”
“like what?” asked chrysalis
“first, that changelings just don’t feed off emotions of love from someone they disguise themselves as. They feed off positive emotions from all around them. The disguise is just a formality.” Said Celestia “second, a missing piece of the prophecy was found.”
“a missing piece?” inquired Layton “how curious.”
“’but peace will only truly come when the two who lead seek to rectify their mistakes.’” Recited Celestia
“get to the point, Celestia!” said chrysalis
“I am willing to allow the changelings to leave these catacombs, and live their lives on the surface.” Said Celestia “I realized, with my sisters help, that it was unfair of me to allow discord a second chance, but to not offer a chance to your own people, chrysalis.”
“you truly mean this?” asked chrysalis as changelings slowly started to come out, interested.
“I do. So long as the changelings don’t cause trouble, they will be allowed on the surface in disguise. What do you think, chrysalis? Would you and your people like that?”
“yes…” said chrysalis, smiling slightly “yes, we would.”
Later, after everything had been arranged, Luke, flora, and the professor prepared to return home
“thou art always welcome in this land of Equestria, flora, Luke, and professor Layton.” Said Luna
“yeah! It was fun hanging out with you guys!” said pinkie pie
“you totally kicked those changelings’ butts, Luke!” said rainbow dash
“I’m just honored to have friends like you!” said rarity, smiling. her Persian cat, opal, jumped off rarity’s back and nuzzled Luke’s leg, purring
“meow! Meow!” went Luke. Opal meowed back. Fluttershy gasped happily
“you can talk to animals too?!” she said, flying over
“I can! Yourself?” said Luke happily
“of course! That’s how I got my cutie mark!” said Fluttershy, pointing to the mark on her flank that showed an image of 3 butterflies. Luke looked down at his own flank and gasped “professor, look!”
“well well, my boy!” said Layton happily
“oh, wow! It looks almost like the professors!” said flora
“well, I’m satisfied!” said Luke happily. Everyone laughed.
“before you go, a little parting gift.” Said Celestia. She handed flora, Luke, and the professor each a kind of necklace “these necklaces were based off of the elements of harmony. You see, their new physical forms are those of necklaces with designs that correspond to each of these girls marks. Luna and I decided that those 6 elements carried by twilight and her friends just didn’t completely show all that’s good. So, Luna and I made these. 3 new elements, and the three of you are their carriers. To you, professor Layton, the element of intelligence.” Said Celestia, handing the professor his element “to you, Luke the element of reliability.” She continued as Luke took his own element
“and me?” asked flora excitedly. Celestia smiled
“to you, flora Reinhold, I give the element of determination. It was your quick thinking in the mines and your determination and courage to help Luke that helped to save the day.” Said Celestia as flora took her own element
“shouldst thou ever wish to return to Equestria, simply make a wish on your elements to return, and thou will return here to where thou wish to go.” Said Luna
“wow! Thanks!” said Luke
“thank you for all your help. Remember, you’re always welcome here.” Said Celestia. She cast the spell that sent Luke, Layton, and flora home. They found themselves back in the professors flat
“oh, it feels so good to be a human again!” said Luke, stretching
“I must agree.” Said Layton. Flora quickly looked at the date and time
“oh, thank goodness! My contest isn’t until tomorrow!” she sighed with relief
“wait…” said the professor, looking at the date. He chuckled “it seems while we were gone, no time had passed.”
“what?!” asked Luke. He looked at the clock “wow! Your right! Celestia sent us back to when we supposedly left!” he rubbed his forehead “you know, I’m going to miss being able to do magic.”
“I liked being able to fly.” Said flora. She looked at herself wearing her element necklace “do you think this necklace goes with the dress I’m wearing to my contest tomorrow?” she asked
“I think it might.” Said Luke, straightening his cap. He sat down on the sofa “you know professor, this will be the one adventure we’ve had that I won’t be able to tell my parents about. If I sent them a letter about Equestria, they wouldn’t believe a word!” he said, laughing
“that’s true, my boy. I think for all our sakes, we should keep our latest investigation between the 3 of us.” Said the professor
“agreed.” Said Luke and flora
“now, how about I make us all some tea?” asked flora, smiling.
Uh oh! Thought Luke don’t let flora in the kitchen! “err.. flora, I think you should let me do it.” He said, getting up
“no, it’s ok.” Said flora “I can do it.”
“no, you just go make sure you have everything ready for tomorrow. I’ll make tea.” Said Luke
“alright then.” Said flora, going to her room. Luke sighed with relief “close one, eh professor?”
“handled like a true gentleman Luke.” Chuckled the professor. Luke went into the kitchen and started making tea. As it boiled, he went back into the living room. He traced a circle on the arm of the couch.
“something on your mine, Luke?” asked the professor as he selected a book from the shelf
“it’s just… back in the catacombs…” started Luke. He sighed “professor-“
“no need to apologize Luke.” Said the professor
“I almost killed you professor.” Said Luke
“it wasn’t your fault. You were under chrysalis’s control. You weren’t yourself.” Said the professor
“doesn’t make me feel any less bad about it…” said Luke.
“it wasn’t your fault Luke. Flora and I are just glad you’re yourself again.” Said the professor. Luke gave a small smile “alright, professor.” He said.
Later that night, Luke sat in his bed, writing in his journal. His pen moved across the page. When he finished, he yawned and placed his cap on his bedside table. He lay in his bed, looking out his window at the stars. He yawned again and reached for his teddy bear. As he hugged it close to his chest, he thought and so ends another investigation by professor Hershel Layton, and his apprentice number 1, Luke triton… he yawned again and closed his eyes, falling fast asleep.

Author's Note

and so it ends! for the record, the song that flora sings is the ending theme to professor layton and the diabolical box: iris. big thanks to my super awesome layton obsessed uk friend, tasha rose, aka donniegirl12, for the lyrics! heres the link:
http://www.youtube.com/watch?v=gi7PN1PxhJ0

Rotten Heart and Discord

“I can’t find any passageways! Did you two find any passages?” Shining Armor asked to Layton and Flora.
“I believe we are stuck, because I can’t seem to find anything.” Professor Layton replied.
“But Professor! We must find a way out, we simply must!” Flora replied. “If we don’t, Luke could be in great trouble!”
“And the whole of Equestria would be in great danger as well!” Shining Armor added on.
“Now, now, settle down. We’ll find a way out, I know we will.” Layton replied. “Now, you said that there was an abandoned miner’s shaft somewhere? One that your sister and your wife traveled down to stop you from marrying a fake bride?” Layton asked.
“Yeah. But you said it might be blocked off.” Shining Armor replied. He and Layton started discussing on how to find a way out. Flora sighed and walks off, laying down when she was far enough away ‘oh Luke… I hope you’re okay…’ she thinks to herself. She hears the buzz of insect wings. She looks around, thinking that a bug was nearby. She then saw the figure of a changeling pass by. He sat down himself, not seeming to notice flora. She looked behind her, where shining armor and the professor were still talking, and said quietly to the sad-looking changeling “are you alright?” the changeling looked up. It seemed to be a foal changeling.
“y-yeah…” he said “I’m fine…”
“no you’re not. You’re obviously upset about something.” Said flora
“shouldn’t you be the one upset? You’re the one locked in there.” said the changeling
“true, but I’d hate it if I was stuck underground all the time. I mean, at least I have a chance of being able to leave.” Said flora. The changeling frowned “sorry… that was the wrong thing to say” she continued, blushing
“doesn’t make it any less true…” said the changeling
“hey… why don’t you talk like the other changelings?” asked flora
“what do you mean?” it asked back
“well, the other changelings hiss with their S’s, why don’t you?”
The changeling shrugged “everyone knows I’m different. All of us changelings want out, but I don’t think we need to do anything bad. It’s because we do bad things that the equestrians don’t like us and won’t give us a second chance above the ground.”
“the professor says it’s important to give second chances.” Said flora
“is that professor guy your father or something?” asked the changeling
“no… but some time ago, he adopted me. He and his apprentice were investigating a mystery surrounding my home village. He adopted me from my step mother when they solved what we call “the mystery of the golden apple.” Said flora. She pointed to her cutie mark “which, actually, was me. Whoever was smart enough to discover that I myself was the villages golden apple would be able to be my guardian. Papa died when I was younger, so the professor has always been like a father to me ever since he adopted me.”
“ponies are so weird…” muttered the changeling
“and I could say the same thing about changelings.” Said flora
“…okay, I see your point.” Said the changeling, chuckling “you know, you’re kind of funny.”
“you’re not like the others. You’re… nicer.” Said flora, smiling.
“…thanks.” Said the changeling, giving a small smile as well
“flora?” called the professor
“coming professor!” flora called back. She turned to the changeling “I have to go…”
“come back again tomorrow? It’s nice having someone to talk to.” Said the changeling
“I’ll try.” Said flora. She went back to the professor and shining armor.
With Luke and the others in Ponyville, spike and twilight were searching hard for the book.
“Agh!” groaned twilight “you know what spike? Just send a letter to princess Celestia for me please? I think she has a copy.”
“sure thing.” Said spike. Just then he burped out a puff of flame, a scroll falling into his claw. Twilight levitated it over and read it, her eyes darting to and fro across the parchment “ah, no!” she groaned
“what’s the matter?” asked Luke
“discords on his way…” sighed twilight “the princess is sending him because she thinks he might be able to help.”
“whose discord?” asked Luke
“a spirit of disharmony and chaos. We’ve fought with him a couple of times, but we finally managed to get him to use his powers properly and NOT cause trouble everywhere.” Said twilight. She walked upstairs and came down a minute later, wearing a tiara and levitating a box beside her. “I’ll be back in a bit, I need to go stop by each of my friends’ homes and give them their element of harmony. Spike, while I’m gone, write a letter to the princess and ask her if she has a copy of that book on changelings.”
“you got it, twilight!” said spike as twilight headed out the door.
“spike, what are the elements of harmony?” asked Luke.
“Ummm…” said spike, going over to a shelf “ah, here it is!” and he pulled a book titled ‘the elements of harmony’ “here, that book will explain it all.” Said spike as he handed it to Luke, who got to reading it.
“The Elements of Harmony…the most powerful force in all of Equestria. There are 6 Elements, and they embody all that’s good. But will only work for the one who has that particular trait. There’s kindness, honesty, loyalty, generosity, laughter, and magic. But, also known as friendship. Hmm…interesting.” Luke said as he read aloud.
“Yep! Twilight has friendship, Fluttershy has kindness, Rainbow Dash has loyalty, Rarity has generosity, Applejack has honesty, and Pinkie Pie has laughter.” Spike explained.
“so if this discord person is on our side, why is twilight giving the elements to her friends when I assume she normally keeps them here?” asked Luke
“well, the girls don’t exactly trust discord yet. Well… except for Fluttershy.” Said spike “her and discord actually get along pretty well, since Fluttershy was the only one who actually bothered to give discord a second chance.”. A bit later, twilight came home
“there. each of the girls have their elements and are getting ready. They should be here soon.” Said twilight. “the letter said that discord would also be here soon.”
“let’s hope he doesn’t cause trouble.” Said spike
“please. Discord is all about attention. If there are changelings stealing his spotlight, he’s going to want to drive them out like us. The problem is getting him to do it RIGHT.” Said twilight. Each of the girls arrived fairly soon
“I can’t believe the princess is sendin’ discord…” said applejack
“oh come on applejack, we did reform him.” Said Fluttershy “and personally, I’m glad he’s coming.”
“that’s because you got all buddy-buddy with him!” said rainbow dash “I don’t care if the princess thinks he can help, we can do this without him!”
“he may be able to help find changelings with his powers.” Said twilight. Luke became interested then, but didn’t show it too much. A bit later, there was a knock at the door. When twilight answered it, she saw a unicorn with a brown coat, tail, and beard streaked with gray.
“umm… can I help you?” she asked
“what, you don’t recognize me, miss sparkle?” asked the pony
“oh my, discord, is that you?” asked Fluttershy
“at least somepony recognized me.” Said discord
“did the princess make you do this? I highly doubt you’d disguise yourself on your own.” Said applejack
“as clever as ever, aren’t you applejack? Yes, Celestia did make me disguise myself. She said ponies would be scared to see a draconoquis around. So this was the disguise we agreed upon.” Said discord. He spotted Luke coming down the stairs “and you must be Luke. I was expecting a human.”
“and I wasn’t expecting a pony.” Said Luke
“how clever. You’re not as proper and behaved as Celestia made you out to be.” Said discord “we just might get along, you and me, Mr. triton.” He saw the professor and frowned, sensing something… off.
“say, twilight, I’ve had a bit of a tiring journey, you wouldn’t mind if I got something to eat, would you?” he asked
“she wouldn’t mind at all, would you twilight?” asked Fluttershy
“no. I suppose not. You eat what we eat though.” Said twilight “and we have our elements, so if you cause any trouble-“
“twilight dear, I’m reformed remember? Your words cut me like a knife!” said discord, staging a hurt look. He walked towards the kitchen, giving Luke a small look
“I’m thirsty myself. I’ll go join discord.” Said Luke. He followed discord into the kitchen
“you have suspicions as well?” Luke whispered to him
“something is off about him. There’s something off about you, but with him it’s… different. I know you’re really human, which explains you, but from your friend, I’m not getting that same off feeling. It feels…” said discord
“darker?” finished Luke. Discord nodded
“your intuitive kid. I like that about you.” He said
“thanks, I guess.” Said Luke “so… any ideas on how we can find out whether or not that’s the real professor?”
“I may know a handy little spell. If we’re right, it will break the changelings disguise and show it for what it is. If we’re wrong and that’s the real professor, it won’t hurt him and no one will have to know.” Luke nodded
“I don’t like doing anything behind the professors back, he’s like family to me, but if that’s a changeling, then I don’t have much of a choice. We need to make sure to capture it before it gets away though.” He said
“be ready then. If it’s a changeling, then we won’t have much time once I cast the spell” said discord.
“alright. I trust you.” Said Luke
They went back a minute later. As the girls discussed ideas on their next plan of action, Luke and discord snuck upstairs to where the changeling professor was. Discord took a deep breath and closed his eyes. His horn glowed as he prepared the spell
“get ready, kid.” He said. When the spell was cast, the changelings disguise was lowered. It hissed in anger as it realized what happened. Luke quickly ran, ready to tackle it. The changeling knocked Luke against a wall, where he fell to the ground. The girls went quiet as they heard the commotion. As the changeling went to get away, a purple light shown around It as twilight kept it in place
“not so fast!” she said
“you big meanie! Tell us where the professor is!” said Fluttershy
“yeah! And where’s shining armor too?!” said rainbow dash
“I’m sssssaying nothing!” hissed the changeling “sssshe’d have my head!”
“who, chrysalis? You’re dead if you talk, and you’re dead if you aren’t! if you don’t talk, we’ll take you to Celestia and she’ll make you talk.” Said discord “so, you have nothing to lose right now.”
“catacombssss beneath Canterlot. I’ll ssssay no more!” said the changeling “do what you will, but I’m done talking!”
“always the catacombs…” muttered twilight “discord, make it so this thing can’t get away. I need to send a few letters.” Discord imprisoned the changeling as twilight started sending letters and everyone prepared to trek through the catacombs.
With flora, the professor, and shining armor the next day, flora had kept an eye out for the changeling from the previous day. Finally, he came.
“you came! I was worried you’d forgotten.” Said flora, sneaking over
“sorry it took me so long. My mother had a lot of tasks for me.”
“I wasn’t aware changelings could have children.” Said flora
“we’re not too different from you ponies… it’s just that we look so different we’re forced to cause such trouble… I’ve long given up on trying to convince my mother that we should try for peace. She won’t hear a word of it…”
“it’s always sad when we can’t along with family… in life, family is all you have.” Said flora. The changeling nodded
“what’s your name?” flora asked
“oh… umm…” said the changeling “it’s… umm…”
“what?” asked flora “don’t you have a name?”
“I do… I just don’t like it… its Rotten Heart…” said the changeling quietly
“well, my names Flora.” Said flora
“flora, huh? That’s a pretty name.” said the changeling
“oh, thank you! My mother loved flowers, and her name was a flower too. Her name was violet.” Said flora. The changeling chuckled
“did your family own a flower shop?”
“no. my father was a baron. He and mother died when I was little.” Said flora “I lived in a nice house for a while, and then I met the professor.”
“you know flora, you’re… umm… your very pretty…” said rotten heart
“oh!” said flora, blushing “well… Ummm… th-thank you…”
“I-I’m sorry! I shouldn’t have said that!” said rotten heart “I’m so stupid!”
“no, it’s okay!” said flora “it’s just… the only other person who’s said that is my best friend Luke… he’s the professors apprentice.”
“yeah… mother says that changelings will be sent after him soon… just as soon as she can find a suitable one to take his place and trick the element bearers…” said rotten heart
“poor Luke… I hope he’s okay…” said flora. She paused “oh, my! I really shouldn’t be so worried about Luke, it will strengthen my changeling self!”
“actually, that changeling was forced to flee. Your friend Luke figured her out… same with the changeling we sent to take the professors place. We can’t send more because now they know you guys are here…” said rotten heart
“that’s good then! They should be here soon!” said flora, smiling
“well… there are traps set for them. My mother even set them herself…” he turned away, looking guilty “and… and… Luke’s being saved for last… I’ve been given the task of brainwashing them to serve the changelings when he’s separated from the others… we’re going to force him to kill you and all the others!” flora’s world seemed to stop. she had always thought heartbreak was just a word, but there was a pain in her chest.
“l-Luke…” she whispered “no! no! Luke will fight it! He won’t hurt us!” she said, shaking her head “no! no! it can’t be!” she turned to rotten heart “please! Please! I know I barely know you, but you have to get us out of here! Even if you can’t free us yourself, surely there’s some hidden passage?!”
“I don’t want you hurt flora… I don’t want to disobey my mother, though…” he looked down, his eyes closed. “I’ll tell you where the hidden passage is, but… you have to try and get me my freedom!” he said, looking at flora “please! You know I’m not like the others, and I’ll prove it to however many people I need to! Take me with you! I hate being down here in the dark, I want to run around on the surface with other ponies!”
“I’ll do my best.” Said flora “I give you my word. Now, tell me where the passage is. I can’t let anyone get hurt.”

Author's Note

chapter 3! sorry it took so long, but all the other chapters WILL be uploaded today.