Secret Agent Flutters

by KnightSpiritWolf

Rating: teen
Tags: Gilda, Random, Adventure, Crossover, Doctor Whooves, Original Character, My Little Pony: Friendship is Magic, Other, Fluttershy
Length: 3119

Fluttershy goes on a secret mission with her partner to save Equestria! Will they succeed?

Fluttershy wakes up only to find she is on her way back to her old secret life. She goes on a mission with her handsome partner to save all of Equestria from the evil mastermind in hiding, Tocxi. Fluttershy is the best agent around, nopony knows this except for the whole agency she works for.

Published 2014-03-25 03:00:04 UTC
Last updated 2014-03-25 03:00:04 UTC

Scorchfeather and Zaine

My eyes opened to only see darkness. I didn't know where I was or where I was going, "why can't I see," I wondered out loud, "anyone there!?" I pull something off my face and could see again. I raise my hoof to my eyes and squint to shield myself from the flaming sun. I look around once I am used to the bright light. Two ponies had me tied up and on my way somewhere. They both wore black outfits. I stare at them trying to figure out who they were. One looks behind and sees me.

"Fluttershy," the pony smiles, "you're awake!"

"What do you want from me!? Whatever it is you are NOT getting it!?" Since I am away from my friends and everypony else I feel like I could be myself again... Or old self. The pony pulled down her hood and only to reveal an orange earthpony with a spikey sunset yellow mane and tail, " I'm Scorchfeather!" She winked.

"WHERE am I GOING!?" I felt alive again.

"The same old Fluttershy, huh? I remember you! When I was a filly, you were amazing!" Scorchfeather put her hood back on and faced back the direction the other pony was going.

"And who exactly is this?" I ask, calming down.

"I'm Zaine." He just keeps trotting along.

"Let me say this again. WHERE AM I GOING?!" I huffed. The nice Fluttershy was gone until I knew what was going on and what was happening.

"You will see," Zaine said as he kept trotting along the path, " don't worry about it until we get there."

"How do you expect me not to worry about something! I am tied up and being pulled on a SLED to someplace I don't even know!" I yell at Zaine.

"You will see! It's okay! And yes you are tied up but there was no other way of getting you here!" Zaine protested. He seems to be annoyed easily. That's one thing about this stallion.

"Why is it so important-" I cut myself off as we arrive to a big building. Memories flooded all around me as I closed my eyes and remembered.

"Fluttershy... Fluttershy!? FLUTTERSHY!??!" Scorchfeather screams.

"Oh... What is it?" I ask with my normal voice.

"Welcome back." Zaine and Scorchfeather smile as I gasp in amazement.

"Before I go in there, I want to know about you two. Are you together?" I ask.

"Um... heh no..." Scorchfeather blushes, "no never..."

"Well, okay then." I need more information on these two.

"We should go inside now." Zaine suggests.

"No, I want to know more!" I smile, "please."

"Why do you want to know about us two?" Scorchfeather glares at me.

"Oh, no reason. Just I don't want to go in there and I am wasting your time and my time because I really do not wish to go back there." I remember the past. Me battling Toxci. Toxci, an evil mastermind.

"Toxci, your time of darkness is over!" I glare at her.

"Oh, Fluttershy you make me laugh!" The tall brown mare stood on the other side of the darkened basement. The only source of light came from a cracked open window, "I remember seeing you when you were just a small foal! Your mother would be so happy to see what you have become now!"

"My mother loved me!" I say with a steel sword in my mouth.

"Well, news flash! I killed her! She DID love you. Your right!" Toxci stepped even closer to me, "I am going to kill you too!" Toxci rammed into me. I was too confused too react.

"My hooves slammed into her side and she fell to the ground. I grabbed the sword and jammed it into her side, only to realize that I missed. I tried again. Hit!

"You do realize this is not a very epic battle, right?" I ask Toxci, who now lay motionless on the floor, but stared right up at me, "because I always win. You knew that. Remember our last time we fought? I won that too. Your time is over." I pull the sword out of her side. She moans and winces in pain.

"I will survive. You know that too." Toxci says still not moving from her spot now invaded by blood.

"Yes. I do know that. But every time you heal and battle me, I always win."

"Your time is coming, Fluttershy. The Doctor is coming. Even my apprentice, Gilda knows about this." Toxci warned me.

"But why are you telling me this? How do you know?" I ask even more annoyed.

"I know because I have met the traveling pony with the blue police box. He told me to warn you about this." Toxci winced again and said with weakness.

I gasp and run out of the basement.

"Uh... Fluttershy? Scorchfeather asks.

"Oh... Sorry. L- let's just go inside now." I stutter.

Author's Note

So, I hope this is a good first chapter. I added a few new things to it. Yeah o3o

Agent Smith

Scorchfeather and Zaine take me into the building. I try to get loose of the rope I was tied on and bit down hard on it. A big wave of pain floods my whole mouth, "AAAHH!" I scream quietly. Tears blind me. My loose tooth! That really hurt! I dry my tears and stop struggling to break free of the rope. I can taste the gross bitter blood inside my mouth. I almost threw up. I can't untie this knot with my hooves! It was just too tight!

"Agent Shy. I am Agent Smith," A pony walks up to me as I enter the building, "I'm your partner!" I looked at the pony unsatisfied. The pony was a light brown stallion with spikey dark brown hair. His cutie mark seemed to be an hour glass or something. Then I remembered.

"Agent Smith, may I speak with Agent Shy a moment?" My old boss! Mr. Fluffeh! Yes... That really is his name. I used to laugh at him all the time! Memories came flooding back as I remembered us laughing at his name. Yes, he really did laugh at himself. That's why I liked him the best here.

"Hello, Mr. Fluffeh.. Heh.." I almost laughed my horseshoes off!

"How are you Agent Shy?" he asks. I straighten up ready to answer.

"I am not good! I was brought here on a sled tied up to a few ponies I didn't even know!" I look down at my sore hooves, "and I am still not untied!"

"Oh, sorry Fluttershy!" He unties my hooves. Relief floods over me. I sit down comfortably.

"We need your help, Agent Shy. Toxci is out of prison now and is going to try to toxicate all of Equestria! Please help us Fluttershy. You are the best this agency has ever seen."

I stare at him bewildered. The best? A determined smile came upon my face. I didn't know I would miss doing this. I sigh and swallow the gross blood still in my mouth, "I'll do it! When do I go?"

"You will have to go right away. Let me go tell Agent Smith." He runs off towards the computers. I close my eyes and remember. I relax a bit then open my eyes again. I felt brilliant. I look around the agency. The white rooms and the hard working ponies. Everypony looked busy as usual. Only the technology has changed. Better computers, tracking devices, and even easier ways to talk to anypony. I also remembered why Agent Smith wont tell me about his true self. He doesn't want to mess up the timeline. I know this because of the agency. Time travel is used here but no where else, except for Agent Smith's TARDIS.

Agent Smith came up to me, "you ready?"

"Ready." I start to trot out of the building until...

"Good luck... My daughter." I stop in my tracks. Agent Illiance is my father. I turn around and race over to him and give him a long hug.

"Thanks dad. You don't have to tell me that mother would be proud. You say that every time I get to see you. You don't need to say It again." I smile and release the hug.

"Don't worry! I'll look after her!" Agent Smith smiles at my father.

"I don't need looking after!" I said with a cold tone in my voice as I walk out of the agency, "you will regret breaking out of prison, Toxci, because your only fear is me. You were safer in prison," I mumble, "I'm going to find you."

We trot off towards Toxci's hiding spot filled with determination.

Clutterflim

Me and Agent Smith turn on another dusty road and I stare up ahead angrily.

"So..." Agent Smith smiles awkwardly, "My name really isn't John Smith."

"I know," I keep staring ahead, "before I begin to talk to a pony I don't know, I need to know more about them. I like to research on them. Interesting isn't it, Doctor?" I smile.

"You already know my name, too." The Doctor says in amusement. A ting of guilt and sadness roared deep inside him.

"You're not from around here. You time travel in something called the TARDIS." I say as I looked at the road again. I could almost see Toxci's hideout.

"And what does the TARDIS stand for?" The Doctor raised an eyebrow.

"Time and Relative Dimension in Space." I say un-amused. The Doctor gaped open his mouth wide.

"That's... Right!" He said with his cool accent.

"I also know that you like the hat called a fez. So does my friend, Knight." I smile. Remember that he doesn't want to mess up the timeline again. I am happy that somepony cares for time and space properly.

"I am Fluttershy." I started trotting faster. We we're almost there!

"So, whats so important about you? So many agents were sent on this mission and you are the one who got the biggest send off." The Doctor stared at me. He knew why. I could feel It.

I stopped walking and turned to him, "I am the best agent they have ever seen. I am also an Element of Harmony. I have saved Equestria many times. I have my experience." I stare at him angrily.

"Which Element are you then?" He asks filled with curiosity.

"The Element of Kindness." I say proudly and blink twice.

"You don't seem like the 'kindness' type to me." The Doctor smiled.

"Well, right now you are seeing my bad side." I trot farther ahead.

"Oof!" I went in reverse and bumped into my partner, "s- sorry..." I squeaked. My good side was here again, then?

"Is this your good side? Shy aspect to you, I see. Is that why they call you 'Fluttershy'?" The Doctor hands me his hoof and helps me up, "It's alright." We start walking along again.

"I heard a noise and got scared for a moment there." I say looking around, "I heard hoofsteps."

Suddenly all the air out of my lungs came out and I started panting. I found myself on the damp ground with somepony pinning me down.

"Who are you!?" She demanded.

"I am Agent Shy!" I smack the pony in the face and she falls to her side. I jump on her and pin her down.

"Now who are YOU?!" I demanded with a dark tone. My eyes became bigger and I glared at the pony before me. I used "the stare."

"I- I'm Clutterflim!" Clutterflim closed her eyes. Clutterflim was a gray mare with straight black hair.

"Now, who do you work for?!" I keep staring. The Doctor walks over with a gaped open mouth again.

"I- I work f- for Tocxi!" Clutterflim stutters. I get a shot from inside my saddlebag and push it into Clutterflim's light blue skin.

"What did you just do!?" Clutterflim screams.

"This will make you fall asleep so you wont go getting more help. Well that was easy!" I say. Clutterflim struggles to stay awake.

"That was a bit random." I say relaxing.

'Am I really the best?' I ask myself

I look at the Doctor and smile and he smiles back. We begin running towards Tocxi's hideout. I have defeated her once and so I will defeat her again!

Tocxi

I shush the Doctor as we walk even closer to Tocxi's hideout. I trot up to the door quietly and tap it with my yellow hoof. It opens with a quiet creak. Maybe that's how Clutterflim got out. I walk inside, the Doctor close behind. We stay as close to the cold ground as we can.

"Who's there!?" A familiar voice screams throughout the entire hideout, "I can smell you! Fluttershy?" The voice sounds closer.

"Yes, it's is I, Agent Shy-" I cut myself off and stare at the Griffon before me. Tocxi isn't a Griffon! That's Gilda! Memories of the past swallow me into the darkness and I stare at her with fear.

"Gilda the Griffon!" I force myself to sound fearless.

"Who is Gilda?" The Doctor sounded curious as usual.

"Who is this?" Gilda asked with an angry expression.

"Oh, hello," the Doctor smiled, "I'm the Doctor."

"Oh, yes, the traveling pony in the Police Box!" Gilda looked away then back at us.

"I know why you are here!" Gilda walked forwards a bit, "and I'm not happy about It!" Gilda ran at me with a great force and she knocks me off my feet. I go flailing in the air and fall on the cold floor. Pain burned my stomach and I looked up at her. I still am haunted by that Day of the Darkness, I call It that. Whenever I was walking in Ponyville and bumped into Gilda, she yelled at me! I don't know why but I kept having nightmares about it! I get up on my hooves and charge at her. I suddenly fall limp and she hits me with her large wings. I go blind.

"Fluttershy! Long time no see!" Pinkie Pie gets ready to throw a vanilla cupcake with chocolate frosting at my face.

"Oh, yes." I smile and get ready for the sugary-good taste of frosting to fill my mouth and smother my face.

"Totally!" Pinkie smiles and throws the cupcake. I awake with a jump and the Doctor stood before me.

"Run." He grabs my hoof and we race off somewhere to hide. Gilda roared behind us.

"What's wrong?" The Doctor asks quietly once we were hidden for a few moments.

"I- I keep remembering a dark memory of the past with me and Tocxi, I mean Gilda!" I say still frightened out of my hooves.

"You can do this. Don't let the past haunt you," the Doctor suddenly looks to the floor, "even if it's somepony you love."

"Somepony you love! Doctor, what's wrong? Gilda sneered, "you loved somepony once didn't you!? Roseluck, wasn't it? Where is she now?"

"She's gone..." the Doctor stared at her with such power and anger. I stared in amazement.

"But where?" Gilda stepped forward.

"Somewhere safe!" He grabbed a peculiar object from his saddlebag and pointed it at her. It made an odd buzzing noise. Gilda hunched down and winced. Still, the Doctor stood there. It felt like hours.

"Doctor! You can stop now!" I joined in, "Doctor!" The noise stopped and he put the object back. He stepped back and looked at me.

"You need to go out there and defeat Gilda. You have too. I have seen the future. This is a fixed point in time. They can't be changed. I'm sorry." The Doctor stared at me. 'Fixed point in what now?' I thought hard for a moment.

"Something is going to happen. I can see it in your blue eyes." I stared back at him, "what is going to happen?"

The Doctor sighed with a ting of sadness, "Y- you might now be able to fly again." he forced out.

"What... I- N-n-no!" I sigh and fix my gaze on Gilda then back at the Doctor. 'I have to save Equestria...' "I'll do it..." I say, I start trembling with fear. A tear filled with determination falls out of my eye as I face Gilda.

"There you are!" Gilda turned and faced me.

"Good luck..." the Doctor sighs.

I extend my wings and float up. I know what I had to do. Anger pulsed through me. The darkness that had once frightened me shall no longer scare me! I look towards my wings. They were on fire! I didn't feel a flame. I look back at Gilda, trying to look like I knew what was going on. She stared in defeat. The red flame made the dark hideout seem much lighter in the rundown room. I close my eyes. I imagine my friends and smile. My eyes open and I hit Gilda with such a force from my wings. I had too. All of Equestria would be ruined. But now, no. My wings grew brighter as I flapped my wings once and hit Gilda even harder. Darkness swallows me whole. I feel pain. But do I really? Am I dreaming?

I open my eyes. I am in the agency. Wait hold on. The agency hospital. My 5 PFF's stood there. The Doctor was behind all of them.

"Fluttershy! You're all right!" Twilight smiled with relief and exhaustion in her eyes. I must have been out for a while. Pain came from my stomach and wings. I stare at my sore wings. Blood still came out of them. Feathers were torn and the reek of the red blood filled the room. I scrunched my yellow nose.

"But your wings..." Rainbow Dash stared at them, "we know what happened."

"Oh..." I say with such weakness. I didn't think it would come out like that, "Apple Jack, Rainbow Dash, Pinkie Pie, Rarity, Twilight, you all are here for me! I am so sorry for not telling you!"

"Oh, It's mighty fine, Sugar Cube." Applejack smiles with affection.

"I love you all!" I sniff with happiness.

"Well, I have to go now." The Doctor sighed, "see you later, Secret Agent Flutters," he smiled and winked at me then trotted out of the room. I knew where he was going. I will see him later on in my life but as a different looking pony.

Author's Note

Tell me what you think! If you think this is kind of rushed, I do too. You don't have to inform me about it in the comments. As always, thx for reading!