The Mysterious Intruder

by TwishyOTP

Rating: teen
Tags: Fluttershy, Twilight Sparkle, Romance, Drama, My Little Pony: Friendship is Magic, Mystery, Rainbow Dash
Length: 6847

Fluttershy tries to solve the mystery of who broke into her cottage one night and begins to develop feelings for Twilight along the way.

Fluttershy is awoken one night and finds a mysterious intruder in her home. With the help of Twilight and Rainbow Dash she will uncover who this mysterious pony is and what they're intentions were. But along the way Fluttershy begins to experience new feelings for Twilight. Maybe even romantic ones. But is it possible Twilight could feel the same way about her?

PS: This is my first fic so go easy on me :)

Published 2018-11-07 19:40:01 UTC
Last updated 2019-10-14 06:24:20 UTC

Chapter 1

The Mysterious Intruder

Chapter 1

The night was ~~humid~~ sultry. Fluttershy was asleep in her woodland cottage when all of a sudden a loud noise from downstairs awoke her. Fluttershy shot up from her bed in a panic and cautiously headed downstairs to see what was going on. When she had reached the end of the stairs she had nearly fainted at what she saw. There in her kitchen rummaging through her things was another pony in a black hooded cloak. Fluttershy froze, paralysed with fear.

“Am I being robbed?” she thought.

As she sat there confused suddenly she heard another noise, this time from upstairs. She looked up and saw Angel stumbling around looking for food. She would have laughed had she not been so afraid. Suddenly the mysterious pony glanced over at Fluttershy and quickly dashed out of the back door to the cottage. Being that the room was very dark and because how quickly the pony had run away Fluttershy wasn’t able to get a good look at the intruder. She had however noticed that the pony whoever they where was a unicorn. Fluttershy sat silently for a moment lost in thought.

“Who could that pony have been? And why would they break into my home?”.

She continued to ponder until she heard a knock at the front door.

“Leave me alone!” she yelled.

“What in Equestria are you talking about?” The pony responded in a familiar voice.

Fluttershy walked up to the door and peered out the window. Outside was a very confused looking Rainbow Dash.

“Rainbow Dash?... I-I’m s-so sorry, I didn’t realize it was you,” she said nervously as she opened the door.

“Is everything alright shy? I was just passing by and I heard loud noises coming from here”.

“Well u-um you see Rainbow I think somepony broke into my cottage.”

“What!” Rainbow said, shocked.

“Well I was asleep and I heard a loud noise that woke me up. So I decided to head downstairs to see what it was and I saw a hooded pony in my kitchen”

“Seriously?” said Rainbow in a now very concerned tone.

Fluttershy simply nodded.

“Do you have any idea who it might have been?”

“ I don’t know dashie, all I know for sure is that it was a unicorn.”

Rainbow Dash’s expression suddenly turned from concerned to angry.

“Yeah well when I find out who did this they’re gonna be sorry for messing with my friend!” She said threateningly.

“H-hold on a second dashie,” Fluttershy said nervously. “Maybe it was some kind of misunderstanding”.

“Misunderstanding!? Law abiding ponies with good intentions don’t show up in your house in the middle of the night in black cloaks shy. There is no way this was a misunderstanding”.

The two ponies sat there in silence for a few a few moments until Rainbow spoke up again.

“Say shy, why don’t you come stay at the castle tonight? You’ll be safe there until we can figure out what happened.”

“Yeah that sounds like a good idea Rainbow,” she responded shyly.

With that said Fluttershy gathered some of her things and left with Rainbow dash to the castle. Not before saying goodbye to her animals that is.

It was very late once they had reached the castle and Fluttershy was almost too tired to worry about the break in. The two pegasi entered the castle surprised to see Twilight Sparkle still awake and looking through several books.

“Twilight?” Rainbow said, surprised.

“Rainbow Dash? Fluttershy? What are you two doing here at this hour?” The unicorn responded.

The two then proceeded to explain what had happened to Twilight.

“A break in?” Twilight said in shock. “But who would do such a thing? And to Fluttershy no less.”

Twilight pondered for a moment before turning to Fluttershy and saying

“Fluttershy I promise that we will get to the bottom of this. We will start investigating first thing tomorrow morning.”

Fluttershy nodded and smiled ever so slightly. Fluttershy and Rainbow were heading to bed when Rainbow turned around to look at Twilight.

“Say Twilight?”

“Yes Rainbow?”

“Why were you up so late yourself?”

“Oh well you see Rainbow I was studying a new type of magical theory I had just discovered and I was fascinated by how...” Twilight stopped as she was cut off by Rainbow.

“Okay okay I get it... Egghead.”

The three ponies all laughed in response before finally going to bed.

Chapter 2

Chapter 2

Fluttershy was restless in her bed. So tired yet she could not sleep. Haunted by the pony dressed in black that she had caught in her home.

“Who?...What?...Why?” She thought. “You need to calm down Fluttershy. Twilight said she would get to the bottom of this and she will. Everything will be back to normal in no time,” she thought as she finally began to relax and slowly drifted off to sleep.

The next day the shy pegasus was awoken to the sound of Twilight pacing and mumbling to herself.

“Think Twilight. Do you know of any unicorns that have malicious intent?” Twilight asked herself.

“Um Twilight?” Fluttershy said startling the alicorn.

“Oh good morning Fluttershy! I hope you slept well last night.”

“As well as I could Twilight”

“Good to hear shy.Now about the investigation I believe I have narrowed our suspect down to only 3000 possibilities!” Twilight said enthusiastically.

“3000? That’s so many ponies,” Fluttershy said confused.

“ I know it may sound like that Fluttershy but that’s actually a very small amount considering how many suspects I started with.”

“How many did you start with?”

“You don’t wanna know.”

The two ponies chuckled. Rainbow Dash entered the room.

“So Twilight did we catch them yet?” She asked.

“Oh Rainbow we’re very close,” Fluttershy said enthusiastically. “Twilight has the list narrowed down to just 3000 suspects.”

Fluttershy and Twilight burst into laughter as they saw the confused look appear on Rainbow’s face.

“Well I hope the process speeds up a little,” Rainbow said, frustrated.

“You can’t rush these things Dash, Investigations like these take time. Besides we don’t have any leads other than the pony is a unicorn,” Twilight responded.

“Fair point,” Said Rainbow Dash.

“Well in any case we need to gather more evidence and the only way to do that is by investigating Fluttershy’s cottage,” Said Twilight.

“Alright well you two go on ahead I promised Scootaloo I would hang out with her today,” Rainbow Dash said as she headed towards the door.

“See you later Rainbow Dash,” Fluttershy and Twilight said in unison before giggling as Rainbow left.

“Well we had better get going,” Twilight said.

Fluttershy nodded as the two headed out the door and towards the cottage. They soon arrived and Fluttershy was taken aback when she saw the state of her kitchen. She hadn’t been able to notice the mess last night as it was too dark to see clearly. The kitchen was in quite a state indeed. There were broken dishes on the floor, Drawers left opened, and a very upset looking Angel in the middle of it all.

“Wow,” Twilight said. “They sure made a mess of things huh?”

“U-huh,” Fluttershy responded.

“It’s still odd though. What could they have been looking for? And in your kitchen no less?”

“I wish I knew Twilight.”

Twilight paused for a moment as she noticed the worried look on Fluttershy’s face.

“Fluttershy I know this must be frightening for you and all but I promise you that things will be okay. I promise I won’t stop until I find out who did this.”

Twilight was slightly startled as the Pegasus enveloped her in a very warm embrace.

“Oh thank you so much Twilight. You really are the best friend a pony could ask for.”

“No need to thank me shy. I’m just doing what’s right.”

Fluttershy smiled warmly at her friend.

“Twilight sure is an amazing pony,” she thought. “And a beautiful one too.” Fluttershy paused. “Did I really just think that? I guess it’s not that strange right? She is my friend after all an there’s no denying that she’s beautiful... and smart, and courageous... and funny... and caring, and an incredible frie... wait a minute. Do I have a crush on Twilight???”

Fluttershy had been so lost in thought that she hadn’t realized how much time had passed.

“Um Fluttershy? Are you going to let me go now?” Twilight said in a slightly confused tone.

Fluttershy had just realized that she had been hugging Twilight this whole time.

“Oh a y-yes, s-sorry Twilight,” she said as she blushed heavily.

Twilight couldn’t help but chuckle a little.

“Fluttershy sure is cute sometimes.”

Chapter 3

Chapter 3

The rest of the day remained mainly uneventful for Fluttershy. Her and Twilight had checked and double checked for any possible clues but had still not found anything. As the hours began to pass by Fluttershy became more and more discouraged.

"How are we ever supposed to find out who did this?" She thought. "And how am I ever supposed to have peace of mind if we don't find out?"

"Ugh this is pointless!" Twilight said in frustration, interrupting Fluttershy's train of thought. "How are we ever supposed to find out who did this without any evidence? And how are we supposed to find any evidence?!"

"You're right Twilight," Fluttershy said as tears began to well up in her eyes. "This whole thing is pointless. We'll never figure out who did this," She continued, now sobbing.

Twilight rushed over to her friend and gave her a warm hug.

"Oh Fluttershy I'm so sorry. I didn't me to be so negative about it. I was just so frustrated because we haven't been able to find anything all day. I promised you that I wouldn't stop until we figured this out and I intend to keep that promise. So please don't cry Fluttershy."

"D-do you really mean that Twilight?" Fluttershy responded.

"Of course I do," Twilight said as she brushed the tears from Fluttershy's eyes.

Fluttershy responded by returning the embrace and squeezed Twilight so hard it nearly hurt. This was somewhat surprising to Twilight but she didn't mind it at all. In fact she enjoyed it. Twilight had always felt differently about Fluttershy than her other friends. She wasn't sure why but she felt more comfortable around Fluttershy than anyone else. Something about being around her always seemed to make Twilight feel better. The two continued the hug for a few minutes which felt like hours as they remained silent.

"I'm a pretty lousy friend aren't I?" Twilight asked.

"No you're not!". Fluttershy yelled which caught Twilight off guard. "You're an amazing friend Twilight! You're doing your best to help me when you have no obligation to because you're concerned about me. Since we've been friends you've been nothing but kind and caring to me. So don't you ever say that you're a lousy friend! You're my best friend and you always will be."

"Fluttershy I don't know what to say. Thank you"

Twilight was about to speak when out of the corner of her eye on the back door to the cottage she spotted a tiny piece of black fabric. It appeared that it had been snagged on the door as the intruder made their hasty escape.

"Fluttershy look!" she exclaimed. "We were so focused on searching the kitchen that we must have missed this." She said as she levitated the piece of fabric towards her."

"Oh Twilight that's amazing! We finally have some more evidence!" The pegasus said excitedly. "Now what should we do with it?"

"I know a pony who knows a thing or two about fabric," said Twilight.

"I think I know who you're referring to," Fluttershy said with a smile.

As the day dragged on the two ponies had now arrived at the Carousel Boutique to see Rarity. Twilight knocked on the door and it was promptly opened by Rarity.

"Hello darlings, what brings you here at this hour?" Rarity asked cheerfully.

"We were hoping you could tell us something about this," Twilight said as she showed the piece of black fabric to Rarity.

Rarity examined the fabric more closely for a few moments.

"As a matter a fact I do know something about this fabric dear," she said.

"H-how is that i-if you don't mind my asking?" Fluttershy asked timidly.

"Well, because I made it."

"You did?" Twilight and Fluttershy asked simultaneously.

"Yes of course darling. I could recognize this stitching anywhere."

"Do you know who bought the cloak it came from?" Twilight asked.

"I'm not exactly certain Twilight. Why did you want to know?"

"Well um you see Rarity somepony broke into my cottage last night and this came from the cloak they were wearing," Fluttershy explained shyly.

"Somepony did what?!" Rarity asked in shock. "I swear some of the ponies in this town are crazy. But anyway I really can't remember who I sold that cloak to. I've sold quite a few of that make. Do you know anything about this pony you're looking for?"

"All we know so far is that they are a unicorn," said Twilight.

"Hmm, well I'll have to think on it. Rarity said as she pondered. "Anyway good luck to you on your search"

"Thank you Rarity," Fluttershy responded.

With that the two ponies left the Boutique and headed back toward Fluttershy's cottage. On their way there however Fluttershy began to notice that it was getting very late.

"U-um Twilight?"

"Yes Fluttershy?"

"Would it be alright if I stayed with you at the castle? Just until we figure this out."

"Of course you can Fluttershy," said Twilight.

"Thanks so much," Fluttershy said, beaming.

The two then made there way to the castle. Spike was there to great them at the door and they were soon inside. It was now almost midnight.

"Well I guess we had better get some sleep," Fluttershy said in between yawns as she headed towards her room.

"Hey Fluttershy?" Twilight asked.

"Yes Twilight?"

"D-did you really mean what you said back at the cottage? About me being your best friend and all?"

"Every word Twilight, every word," Fluttershy said before finally heading off to bed.

Twilight was somewhat surprised by her confidence.

"I never new she thought that about me?" Twilight thought. "I'm glad she thinks of me as her best friend. She really is such a sweet pony and how thoughtful of her to say that."

Twilight went into her room and was now lying on her bed. She began to ponder about her experiences with Fluttershy and her other friends.

"I think she's my best friend too." She smiled before drifting off to sleep.

Chapter 4

Chapter 4

Fluttershy was now lying down in her bed. She finally felt a sense of security being in the castle again. Just knowing that Twilight was nearby made her feel much more relaxed. As she lay in her bed she began to drift off to sleep surprisingly easily considering the circumstances. At last it seemed that she was able to find some peace. However it wouldn't last very long.

Fluttershy suddenly awoke, still lying in her bead. A sense of fear slowly crept over her. Suddenly out of the corner of her eye she spotted a pony in her room. They appeared to be the same pony she had seen breaking into her cottage. They were dressed in the same black cloak and as Fluttershy looked closer she saw a horn protruding out from it.

"It's the same pony? But how are they here? How did they find me again? Something isn't right."

Fluttershy was about to cry out for Twilight but she couldn't speak. Now matter how hard she tried she was utterly silent. It was then that she noticed that she couldn't move either. It was as if she was paralyzed with fear. She soon began to panic as the mysterious figure began to approach her. She felt completely helpless.

"What's going on?! What's happening?" She thought as the figured slowly inched closer and closer to her.

Now they were so close she could almost see their face clearly. Fluttershy's heart began to beat faster and faster. Just as she was about to see their face suddenly...

Fluttershy shot out of her bed still in a panic. She was breathing so heavily she was almost hyperventilating.

"I-it's okay Fluttershy. It was just a nightmare" She thought, trying to calm her self down.

It seemed that her efforts were futile however, as she continued to tremble, unable to shake the feeling of terror she had just experienced.

"Great, how am I supposed to get any sleep now?" She thought, frustrated.

Meanwhile Twilight was fast asleep in her room. She was having one the best night's sleeps she had had in years. It was as if nothing could disturb her, that is until she was abruptly awoken by a knock at her door of course.

"Spike! How many times have I told you not to interrupt my beauty sleep?" Twilight said in a very frustrated tone.

"O-oh I'm terribly sorry Twilight. I didn't mean to upset you." Fluttershy responded timidly.

Twilight could tell that her friend was afraid, just by how she spoke.

"Fluttershy? I didn't realize it was you. You wouldn't believe how many times Spike has woken me up in the middle of the night. Sometimes I don't know what to do with him. But anyway is there something you need?"

"Oh well um... y-you see, I know this may sound silly but I kind of had this really terrible nightmare and I was wondering If maybe I could sleep here? W-with you."

"That doesn't sound silly at all Shy. It's perfectly understandable that you'd be having a hard time given all that you've been through. So of course you can sleep here." Twilight responded cheerfully.

"Oh really? Well I'll just sleep over here on the floor than..."

"Nonsense!" Twilight said, interrupting her friend. "You can sleep in the bed with me"

"Really? Are y-you sure you wouldn't mind?"

"Of course not shy! That's what best friends are for."

Being referred to as Twilight's "best friend" made Fluttershy blush. She could tell by the way that Twilight said it that she was being sincere.

"Well alright then." Fluttershy said with a smile on her face as she tucked her self in next to Twilight. The two laid there for a brief moment before Twilight spoke.

"So Fluttershy, I've been wondering?"

"Yes Twilight?"

"I've always thought that Rainbow Dash was your best friend?" Twilight asked curiously.

"Well she was when we were younger. She always stood up for me and I still consider her a very close friend. But with you it's different."

"How so?"

"I don't really know how to explain it. It's just that something about being around you makes me feel comfortable. I always feel like I can be myself with you Twilight. It's almost like my shyness begins to disappear or something when I'm with you. I think it's because you're so kind and genuine to me. With Rainbow it's a bit different. It almost feels like she needs to pretend to be some invincible hero for my sake, to make me feel comfortable. She's always seen me as someone she needs to protect."

"And it doesn't feel that way when you're around me?"

"No it doesn't. I feel like we have a different kind of friendship. You know what it's like to have trouble being around other ponies. You didn't even have any real friends before moving to Ponyville. I think that's why we get along so well. In a lot of ways we're the same."

"You know I've never really thought of it that way Fluttershy. But it does make a lot of sense to me now. I've always felt a certain comfort around you too."

Twilight rolled over in the bed and was now facing Fluttershy. Fluttershy smiled at her and she smiled back.

"You know, I'm really proud of you for opening up so much to me," Said Twilight.

"Thank you Twilight. I never find it easy to open up at all. Normally I wouldn't be able to share any of this but with you here it's much easier."

Twilight leaned over and hugged Fluttershy.

"Best friends forever?" Asked Twilight.

"Best friends forever," said Fluttershy.

"Well I guess we had better gets some sleep." Twilight said.

"I guess so" Fluttershy said as she chuckled.

It was now very late indeed. Far too late for anypony to still be awake. As the two said there good nights they slowly but surely began to fall asleep. Fluttershy was still a bit shaken up from the nightmare but she felt much better now.

"Best friends forever." Fluttershy thought to herself."But what if I want to be more than best friends?"

Now completely exhausted Fluttershy finally fell asleep.

Chapter 5

Chapter 5

It was late morning when Twilight had awoken from her sleep. It was much later in the day than when she usually woke up. She yawned before slowly opening her eyes and looking over at Fluttershy. She had noticed that her friend was still hugging her.

"Dawww she's so cute! Twilight thought. "And pretty too... like really pretty."

It was the first time Twilight had really thought about Fluttershy that way. Twilight's own thoughts were beginning to confuse her. She would have thought on it further had her train of thought not been interrupted by Fluttershy waking up.

"Mhm good morning Twi," Said Fluttershy, groggily.

"Good morning Shy!" Twilight said enthusiastically. "Did you sleep well?"

"Yes I did surprisingly." Fluttershy said with a giggle.

"I'll make us some breakfast," said Twilight.

"Oh, that's okay Twilight. You don't have to do that."

"Of course I do, you're my guest and my best friend. It's no trouble," Twilight said with a bright smile.

"Okay then," Fluttershy said as she smiled back at her.

Twilight headed to the kitchen to start making breakfast and ran into Spike along the way. He was in the kitchen very obviously trying to sneak a few extra gems for himself.

"Morning Spike!" Said Twilight.

She laughed as he jumped dropping all of the gems as he did so.

"Uh g-good morning Twilight," he said, fearfully.

"Just make sure you don't eat them all in one sitting," Twilight joked.

Spike simply nodded.

Twilight wasn't the best cook in Ponyville by any means but she could get the job done. Fluttershy entered the kitchen as Twilight was busy cooking. She smiled and waved at Spike, who waved back at her. She waited patiently for a while until Twilight had finally finished cooking. The two sat and ate for a while until they heard a knock at the door.

"I'll get it," said Twilight.

Twilight trotted over the the door and opened it. Outside was Rainbow Dash.

"Hey Twilight, did you find out who did it?" Rainbow asked hastily.

"No Rainbow I'm afraid we haven't yet. We did however find a new clue," Twilight responded.

"Really? That's awesome! So what is it?"

"Well we found a piece of fabric from the intruder's cloak and brought it to Rarity. She said that it was from a cloak that she made," Twilight explained.

"So did she know who's cloak it was?" Rainbow asked curiously.

"Well, she said that she needed to think about it."

"Well what are we waiting for? Let's go to the Carousel Boutique and ask if she's figured it out yet!" Rainbow said with a sense of urgency.

"Well you see we were just eating and..."

"That's okay Twilight, it's really no trouble," Fluttershy said, interrupting Twilight.

And with that the three ponies were headed to visit Rarity once more. When they arrived Rarity greeted them at the door.

"Well hello again Darling," Rarity said, cheerfully. "I've been going through my records all day and I've put together a list of unicorns who have purchased cloaks from me," She said as she levitated a piece of paper with several names written on it over to Twilight.

"Thank you very much Rarity! said Twilight. "I'm sure this will be very helpful to us."

"Don't mention it Twilight. Oh, and good luck with your investigation," Rarity said as she closed her door.

Rainbow Dash and Fluttershy looked over Twilight's shoulders to see who's names were written on the list. Although it had narrowed down the suspects considerably it was still a very long list, and it probably wasn't 100% accurate either. Twilight examined the paper and began to read off the names out loud to herself to see if any caught her attention.

"Let's see here," she said. "Lyra, Dr Whooves, Starlight Glimmer, Viny... Wait? Starlight Glimmer? Maybe we should ask her if she knows anything about this."

"Sounds good to me," replied Rainbow Dash.

Fluttershy simply nodded in agreement.

"Alright so where can we find her?" asked Twilight.

"I think she said something about hanging out with Maud today." Rainbow replied.

"Alright, well let's get going then," said Twilight.

After a short walk the three ponies had arrived at the crystal cave where mod lived. There they found Maud Pie bearing the same blank expression she always had on her face.

"Hello," Maud said, plainly.

"Hi Maud, we were just looking for Starlight," said Twilight.

"Starlight your friends are here to see you." Maud called out, in her typical monotone voice.

After a brief moment Starlight entered the room.

"Hi you guys! What brings you here?" Starlight asked.

"Have you ever bought a black cloak from Rarity?" Rainbow asked bluntly.

"Well yes actually. Why did you want to know?"

"A unicorn broke into Fluttershy's cottage a couple of days ago and they were wearing a black cloak," Twilight explained.

"Funny you should say that because the black cloak I bought from her actually went missing about a week ago," said Starlight.

"Missing?" Twilight, Fluttershy, and Rainbow said in unison.

"Yeah I wish I could help you more but that's all I know," said Starlight.

"No, that's okay Starlight. It's quite possible there may be a link between your missing cloak and our suspect," Twilight responded.

"Well if you need my help with anything just let me know," Starlight said.

"Thanks Starlight," The three ponies responded.

They then said their goodbyes and were soon headed back to the castle. When they arrived the sun was already beginning to set. The three ponies were all surprised at how quickly the time had passed.

"Well I had better get going you guys," Said Rainbow.

"Yeah see you tomorrow," Twilight said.

"Goodnight Dashie," said Fluttershy.

"Goodnight guys," Rainbow said as she took her leave.

Twilight and Fluttershy were once again alone as it appeared that Spike had already gone to sleep. Fluttershy stared at Twilight. She could tell just by looking at her that she was deep in thought.

"She sure looks cute when she's thinking about something," she thought. "She spends so much of her time trying to solve this crazy thing just for my sake, and she hasn't once asked anything in return. Maybe she was supposed to be the element of kindness and things just got mixed up." She chuckled to herself. "I wish I could be around her all the time. Maybe I can be?"

"Is everything alright Fluttershy?" Twilight asked.

"O-oh yes! I was just thinking about something," Futtershy said as she blushed.

"Well I guess we had better get some sleep," said Twilight.

Twilight was about to leave the room when Fluttershy spoke up.

"Oh um Twilight?" she asked timidly.

"Yes Shy?"

"Would it be alright if I slept with you again tonight?"

"It would be more than alright," Twilight said with a wink which made Fluttershy blush heavily.

"Is she flirting with me?" Fluttershy thought.

The two then headed towards Twilight's room.

"Was I just flirting with her?" Thought Twilight.

As the two crawled into bed Twilight felt a slight blush on her cheeks as Fluttershy snuggled into her.

"Do I have a crush on Fluttershy?"

Chapter 6

Chapter 6

Rays of sun lit up Twilight's room as she began to stir in her bed. She was finally beginning to wake up and it appeared that she had slept in once again. She slowly opened her eyes, yawned, and then turned her head to check on Fluttershy. The Pegasus was still cuddling her, sleeping peacefully. Twilight found the sight to be so adorable that it almost drove her crazy.

"Dear Celestia she is cute," Twilight thought. "Okay I think it's pretty clear now, I definitely have a crush on her. But how come I haven't noticed until now?" Twilight thought for a brief moment. "Maybe because I haven't been this intimate with her before? Or because I've spent so much time with her in the past few days? I guess none of that really matters now."

Twilight was taken away from her thoughts as she noticed Fluttershy stirring next to her.

"Good morning Twilight," Fluttershy said as she yawned.

"Morning Shy."

Despite the fact that Fluttershy was awake she continued to cuddle into Twilight as the two lay there for a few moments. Although Twilight was really enjoying cuddling with Fluttershy she felt as though she should probably say something to keep things for getting weird.

"Um Fluttershy? do you think maybe we should get up now?," asked Twilight.

"Oh I'm s-sorry Twilight. D-do you not like the cuddling? I can stop if you want."

"NO!" Twilight yelled surprising Fluttershy. "Uh I mean no of course not. I love cuddling with you."

"Y-you do?" Fluttershy asked as a huge blush began to appear on her cheeks.

"Uh yeah," Twilight replied.

"Well that's good. I guess I kinda sorta maybe l-love cuddling with you too," said Fluttershy.

Both ponies were now clearly blushing.

"Is she blushing?" Fluttershy thought. "But why is she? Does she feel the same way about me? No it couldn't be that, could it?"

Suddenly there was a knock at the door.

"Wake up sleepy heads, it's almost noon," Spike said.

"Coming Spike," Twilight responded.

Twilight broke out of Fluttershy's embrace and began to get out of bed. She noticed the disappointed look on Fluttershy's face.

"Does she really like cuddling with me that much?" Twilight thought.

Meanwhile Rainbow dash was flying over Ponyville on her way to catch up with Twilight and Fluttershy about the investigation. For some reason it was all she was able to think about for the past few days. Throughout the years Rainbow had always been very protective of Fluttershy. Ever since they were just fillies she took it upon herself to look after her friend.

"I hope this all gets sorted out soon," Rainbow thought. "This whole thing makes me feel uneasy. What does somepony want with Fluttershy anyway? This had better not be someone's idea of a prank or something"

Rainbow continued to get angrier the more she thought about it. Nothing made her more upset than ponies messing with her friends. Especially Fluttershy. She was so lost in thought that she almost flew right past the castle. She came to a sudden stop and landed right at the castle entrance. She took a moment to clear her head and then knocked on the door. A few seconds later Fluttershy opened the door and greeted her.

"Hey Fluttershy how are you?"

"I'm good Rainbow, I was just wondering if I could talk to you... alone."

"Of course you can. So what's up?"

"Well you see, I kinda..." Fluttershy paused for a moment.

"Kinda what Shy?" Rainbow asked.

"I think I..."

"What?" Rainbow asked impatiently.

"I Have a crush on Twilight!" Fluttershy blurted out.

"You what?!" Rainbow asked, in shock.

"I have a crush on her ok? I want us to be more than friends. Every time I'm around her I feel strange. Like a strange feeling inside. I don't know how to put it in words."

Rainbow just stared at her friend for a moment, unsure of what to say. This had come as a huge surprise to her.

"Wow, you and Twilight huh? I can honestly say I never saw that coming. I didn't even know you liked mares Shy," said Rainbow.

"Well y-yes I do like mares. I always have," Fluttershy responded timidly.

"How come you never told me?" Rainbow asked in a concerned tone.

"I don't know Dashie, it's not exactly easy for me to talk about that kind of stuff. I'm sorry I didn't tell you sooner." Fluttershy said as she hung her head.

"No it's fine Fluttershy, really. But why bring all of this up to me now?"

"Well, I w-was hoping you could give me some advice," Fluttershy said nervously.

"About what?" asked Rainbow.

"About if I should tell Twilight or not," Fluttershy responded.

"Are you kidding? Of course you should tell her. Trust me keeping that kind of thing a secret only ends badly. If you feel that way about Twilight you should tell her," Rainbow said sternly.

"B-but what if she doesn't feel the same way? What if it ruins our friendship?"

"Listen to me Shy, your friendship with Twilight is way to strong to get ruined like that. The only way to make yourself feel better is to tell her."

Fluttershy thought on Rainbows words for a moment before sighing.

"I know you're right Rainbow, but I just don't know if I can tell her," Fluttershy said in a defeated tone.

"Of course you can tell her Fluttershy. Just wait until the moment is right and you will be able to tell her. You're a stronger pony than you give yourself credit for," Rainbow said, attempting to comfort her friend.

"B-but h-how will I know when the moment is right?" asked Fluttershy

"Trust me Shy, you'll know," said Rainbow with a smile.

Fluttershy smiled slightly back at her.

"Rainbow is right" Fluttershy thought. "I'm going to do it! I'm going to tell Twilight how I feel!"

After talking with Rainbow, Fluttershy felt more determined than ever. She had made up her mind and there was no going back now. She was going to tell Twilight. Her only concern now was figuring out the right time to.

"Trust me Shy, you'll know" Fluttershy thought on what Rainbow had said. "But how am I supposed to know?" She thought as her and Rainbow made there way back inside the castle.

Chapter 7

Rainbow Dash, Fluttershy, and Twilight were all seated at the map to discuss the evidence they had gathered so far about the break in.

"So we know that some unicorn stole Starlight's cloak, then used it as a disguise while breaking into Fluttershy's place,"
Said Rainbow.

"That's not exactly much to go off of," Twilight interjected, and continued "We still have no idea what their motive is, or any physical details about them besides their species."

"Is there even a point in trying to find out?" Fluttershy asked timidly. "I-I mean it's unlikely they'll try something again, and I wouldn't want to be a bur..."

"Shy!" Rainbow interrupted. "You aren't being a bother, and it's important that we make sure you're safe."

"Rainbow is right!" Twilight said, sternly. "We care about you Shy, and you deserve to feel safe, and I won't rest until we can make that happen."

Fluttershy blushed heavily at Twilight's words. "Twilight is such an amazing friend and pony," She thought.

"Well maybe we can go to Starlight's room and find some evidence of who took the cloak," Rainbow suggested.

"That's actually a great Idea Rainbow!" Replied Twilight, "I'll go over to Starlight and see what we can find, you stay with Fluttershy in the mean time."

"Actually, I'll go to Starlight, you stay with Shy," Rainbow responded while slipping Fluttershy a quick wink.

"That works for me," said Twilight.

"Me too," peeped Fluttershy, now blushing even heavier from Rainbow's wink.

"Well it's settled then, See you two later," said Rainbow.

"See ya," Shy and Twilight replied in unison.

Rainbow quickly flew through the palace, toward Starlight's room in a flash. The room was silent for a moment, as Twilight and Fluttershy were now starring at each other. A slight blush began to form on the cheeks of both mares, as they made eye contact.

"So, it seems like we're going to have some free time," Twilight said awkwardly. "Is there anything you want to do until Rainbow is done?"

"Whatever you would want to do, I'm happy if you're happy," Fluttershy replied cheerfully with a bright smile.

"She's so cute and thoughtful, it's like she's trying to drive me crazy on purpose." Twilight thought, as her blush reddened. "Well Shy, there is supposed to be large bird migration near the end of town. I was hoping to conduct some research on it."

"That sounds delightful Twilight!" Fluttershy said still beaming with joy.

"Fluttershy seems really confident when she's alone with me, it's almost like she isn't even shy sometimes. I wonder why that is? Do I make her feel comfortable?"

"Well we should get going then right?" Fluttershy asked.

"U-uh yes of course"

The two ponies headed out of the castle, and began to walk to the edge of town. Fluttershy was walking behind Twilight, as she lead them to the migration site. While they were walking Fluttershy couldn't help but stare at Twilight, as she became lost in thought.

"I need to tell her eventually, but how am I ever supposed to know what the right time is. And what does Rainbow know anyway? Has she even had a special somepony before? What if she gave me bad advice?"

Fluttershy's train of thought was interrupted as she bumped into Twilight, knocking the two ponies over. They fell on the grass, and were now facing each other.

"I'm so sorry Twilight," Fluttershy quickly said sounding panicked.

"It's alright Shy, you didn't mean to," Twilight said warmly, and smiled brightly at the mare lying across from her.

The muzzles of the two mares were mere inches apart, and Fluttershy could feel Twilight's gentle breathing. As she starred across at Twilight, Fluttershy could feel her heart begin to beat faster, and her cheeks got warmer. She was starting to have a strange tingle in the pit of her stomach, and she began to get lost in the princess's eyes. For a brief moment it was as if nothing existed in Fluttershy's world, but Twilight's deep purple eyes. The moment however, was cut short as Twilight got up and brushed herself off using her magic. Fluttershy soon followed suit by picking herself up.

"Well anyway, we're here Shy," said Twilight.

Fluttershy looked up in awe at all the beautiful birds of so many different colours. "This is so beautiful!" She exclaimed.

"It's supposed to be one of the largest migrations this year. I'm actually surprised that you didn't know about it considering your an animal expert and all," Twilight said, somewhat confused.

"Yeah, it's just been hard to keep track of things lately with everything that's gone on," Fluttershy sighed.

"Don't worry about that now, we're here to enjoy ourselves," Twilight replied reassuringly. Her words prompted a slight smile from the Pegasus.

The two watched for hours, as flocks of birds flew by. The whole event was quite the spectacle. As Fluttershy watched in awe, Twilight took notes on the flight patterns, estimated numbers, and different species in the migration. Whenever FLuttershy would glance over, and see her friend jotting down notes like a proper egghead, she couldn't help but let out a slight giggle. Time seemed to fly by for the mares, as the sun was now setting, and the final flock of birds flew overhead.

"I wonder what let's them know when to migrate each year? I mean it's never on the exact same date, but it always seems to be at the best time for it. How do they know?" Fluttershy asked.

"That's a good question Shy, I guess they just know when the time is right somehow," replied Twilight.

"W-when the time is right?" Fluttershy asked timidly.

"Yeah, exactly," said Twilight.

Fluttershy paused, and took a deep breath. "Twilight There's something important I need to tell you."

The severity of the Pegasus's tone caught Twilight off guard. "Of Course Shy, you can tell me anything," Twilight stated with confidence.

Fluttershy could feel her heart racing. She knew that this was the time to tell Twilight about her crush, it had to be. She paused for a moment, and took a deep breath. "Twilight I...

Author's Note

Alright so I've finally returned to this story. Due to some things going on in my personal life I haven't really had time to write for this until recently. I can't make any promises, but I'll do my best to keep updates coming as often as possible, and to get the story completed. if all goes well, hopefully there won't be any more long hiatuses. Big thanks to everyone for reading.