Casting it's spell, that I now am under.
Down a forgotten alleyway in Canterlot, stood a sign that once said a famous pony’s name, now crumbling in the street due to disrepair. Only the letter X remained visible on the sign, and only if you paused to stand close to it, squinting in the darkness of the alleyway. As the cloaked figure stepped into the street, rabbit bouncing behind her, she approached the sign and lightly pressed down in it, sending it further into the dirt.
With a soft click, a wall vanished, revealing a passageway leading down some stairs. Fluttershy stepped into the passageway, and continued walking as it closed behind her. Back in the alleyway, the sign slowly rose back into its original position, and silence returned to the alleyway.
“Passcode Timber Bravo,” she spoke as she walked, another wall sliding open as she finished. Stepping into it, it also closed behind her, revealing a dead end. Placing a hoof on the wall, a beam of blue energy passed through it, and it slid aside with another click, revealing the high tech facility hidden underneath Canterlot. Pulling off her hood, she trotted through the large area.
“Private Butterfly, what brings you to our neck of the woods?” A pegasus with a gun strapped to his belt leaned over the desk of the reception, and winked. An older pony, a unicorn with grizzled old hair, rolled her eyes. Fluttershy paused, and narrowed her eyes at the pegasus.
“Hey, since you came all the way out here an all, mind doing me a favor? My wing is a bit lopsided and I could really use someone to clip it, if you know what I mean.” The stallion raised a wing, giving a wink, and Fluttershy smiled warmly tilted her head as she reached under her cloak.
“Of course,” she spoke, bringing her weapon around in one swift movement and shooting her gun at the exposed wing, slicing through some of the feathers and yet missing the part of the wing that was bone and muscle, as it sailed into the wall behind the pegasus.
“Woah!” The pegasus leapt back, falling off his chair and falling to the ground. Fluttershy turned and headed for the elavator situated in the wall, entering it without another word.
“I told ya not to mess with those Privates, yer lucky she’s one of the nicer ones that dun shoot yer greenhorn head off ya neck.” The unicorn righted the chair for the pegasus as he stood up and rubbed the spot the bullet had sliced through his wing. He would be flying awkwardly for weeks.
“Shut it, she was cute.”
“Private Butterfly, as punctual as ever. You will be briefed momentarily, we are just waiting on a greenhorn to get her pathetic ass here.” The commander was a short, brown earth pony with dark black hair and a military outfit on. Slapping Fluttershy over the back, he quickly led her through the long tunnel as she opened her mouth.
“You’re sending me with a greenhorn? For you to contact me this is probably another suicide mission, are you trying to get somepony killed? What did she ever do to you Sarge?” Fluttershy looked down as the commander raised his head, and barked a short laugh.
“As astute as ever Private Butterfly, and trust me, it ain't my idea. High Command ordered this party be a group of five, with at least two unicorns and frankly, we only have greenhorns left. I figure her best bet of survival is with the mare who single handedly defended a base from an entire army by enlisting the help of a rabbit.” The commander once more laughed, shaking his head as he glanced back to the critter in question.
“With that out of the way, meet your team Private. All are ordered to obey your commands for the upcoming mission.” The commander opened a door and allowed Fluttershy to step inside of a small cinema room, seeing three ponies sitting on the seats. Fluttershy glanced them over, and smiled as she recognized two faces.
“Boombox, Stringer, I’m surprised they called you in.” Fluttershy trotted over to the mare with a white coat and blue mane sporting a vinyl cutie mark. Next to her was a gray mare with a music note cutie mark. Both smiled and stood up, greeting Fluttershy as they brought her into a hug, and razzled her on the head.
“Butterfly, why they haven’t called you in on a mission for years now. We were thinkin you retired, what with that devil bunny of yours.” Boombox smirked at the rabbit as Stringer winced, and sighed.
“I do have to apologise for Boombox. Those late nights partying as her cover have affected her personality, what was there to begin with at least.” Stringer glared slightly at Boombox, who chuckled as all three turned to the new face.
“So, what’s your codename?” Fluttershy recognized the gray pony with the buttercup mane instantly, even without the bubble cutie mark. Normally, her eyes were criss crossed but as she saluted them they were straight, and her wings flared as she lowered her hoof.
“My codename is Muffin, Maam!” Muffin took a seat beside the three as they began to reacquaint with each other. Fluttershy smiled warmly and looked to Angel, who glared and tapped his foot. Straightening up, she once more let her eyes grow cold and stern.
Finally, after twenty more minutes, the unicorn stumbled in the door as all four looked to him. The unicorn in question had bright orange hair and a yellow coat that was similar in color to Fluttershy’s. However, it wasn’t that fact that gave the four reason to pause. It was the fact that this unicorn was a baby.
“Is there something on my face?” She spoke, rubbing her hoof to check she had nothing. Her body was dressed in very light baggy clothes that were similar to Fluttershy’s, but designed for her. Boombox stood up, and laughed.
“Pumpkin Cake? You’re kidding right? Are we gonna have to change ‘er diapers too now?” Boombox raised her head back and laughed as the foal narrowed her eyes, and pulled out a miniature shotgun and fired, right beside Boombox’s ear, shaving off just enough to cause it to bleed.
“I believe she’s made her point. Private Butterfly, this is the finest recruit in our unicorn division. Graduated top of the ranks, and at the lowest age we have ever seen. Her codename is Lantern, I will now begin the briefing.” The commander moved to the front of the room as Lantern took a seat beside Fluttershy, Boombox taking a seat as well, glaring at the foal.
“Right, 54 hours ago a covert group headed into the Griffin Kingdom to receive a package of intel. This group consisted of five ponies, one of them being my daughter. At exactly midday, their radio went silent. We have sent to teams after them, both failed. We’ve lost good ponies trying to reclaim that intel.” The commander’s ears flopped down as he looked away.
“I won’t sugarcoat it, those ponies are most likely captured, or worse. Your mission is twofold; find the intel and return it to us, and search for those who went missing. That intel has top priority, and should be transported via unicorn magic as soon as it is in your possession. Are we all clear?” The commander paused, and all saluted.
“Then I leave how to tackle this mission to you Private Butterfly. You all know where the armory is. Saddle up, your teleportation spell leaves first thing in the morning. Diiiismissed!” The commander saluted, and all stood up, saluting back. As the Commander left, all turned to Fluttershy as she quickly pulled out a map, pointing out the location they had lost radio contact with group Alpha.
“I want silencers on all low power guns, and bring something powerful in case it ends in a gunfight. Everypony is to pack two medkits and unicorns are to keep their magic to healing and protection spells unless otherwise stated. Pack light, but bring plenty of ammunition as we may not see much chance to regain it. With all that said, get some rest, and don’t be late.” Fluttershy glanced to Lantern, who saluted, giving a nod. All turned and left the room, heading for the elevator.
“Yo Fluttershy, I was wondering if you know what Tank would like for his birthday, is there some special Tortoise treat?” Rainbow Dash knocked on the door, blinking as no answer came. Opening it, she found it unlocked, and looked around inside. Closing the door, Rainbow Dash flew into the air and peeked in all the windows.
“That’s strange, Fluttershy is never out at night. Something feels fishy, I better go get Twilight.” Rainbow Dash turned, and flew to Twilight’s house.
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That's the most strange but awesome team of ponies I've ever seen!
5167996
Why thank you
Hum... I admit that my suspension of disbelief is pretty stretched right now. Vinyl and Octavia , why not , even if it's pretty suspicious to have four elite agent on the leave in the same town (if this is your cannon that Vinyl and Octa live here , that is.) ; but Pumpkin Cake is kind of unbelievable. Granted , we do not have a timeline , but she is decribed as a baby , not as a foal , which means that she is at best barely older than she is in the show. A foal like Sweetie Belle would be more believable , abeit still barely believable.
And Ditzy well... nothing to say , as her cover might just be that ellaborate.... or she will miss each shot and jinx the mission.
The enemy won't suspect a thing.
What do you mean by Derpy/Dinky? Is agent muffin bringing her kid along too?
i woulld have go for " bright eyes" as the codename for derpy, giving her bad eye the ability to detect inmediate danger.
5168446
Oops, I meant Derpy/Ditzy
5168136
Sorry about that, but that's just how I decided to do it. Also, foal means baby horse. I think you're thinking of filly.
5169909
Ah yes , filly , my bad.
I get the feeling that you decided to write this story thinking "This is going to be so badass that they are going to shit pure manliness coated bullets while instantly growing a beard. With explosions and ninjas commando in the background."
And even if I don't like the baby commando part , that's enough for me to continue to read.
5169982
Hahha
Kinda
I am writing a story here, with the main purpose being Fluttershy and badassery, but really I just wanted to grab a unique team, and when I was searching unicorns and saw Pumpkin was a unicorn, I was like 'yes', and that was that. 
Alright I have a peeve, if Fluttershy is this Ultra Badass Agent, but she is ranked as Private and her C.O. is a Sarge this seems inappropriate as you have already put Flutters on a pedestal. These ranks seem... inaccurate to what you've shown so far.
With Pumpkin, is he aged up to at least CMC's age or is he still a foal? Because even for me that seems extremely odd... unless he was augumented as such, but even then, foals won't survive an augumentation process.
I'm ususally pretty open-minded about everything, but that's only if there is at least a single plausibe reason why it's possible. It can be vague for all I care just give an explanation.
Regardless, I like the story so far. Keep it up!
The down thumbs aren't down yet.
I will be watching 
5172589
Well, considering during the episode where PP babysits they seem to have an idea of what is funny and what is just sad(A baby wouldn't pause and then cry upon seeing PP's performance) they must have some sort of intelligence beyond a baby's.
I'm planning on explaining as such next chapter, except not in as much detail.
As for the ranks, apologies. I'll search up the proper ranking when I have time.
5173559
I am not quite sure about that, as I have nieces and nephews that I babysit a lot and as any baby or foal, has a set of things they like and don't like. One child could love being thrown up in the air, but the other crys whenever you do it. As with any intelligent creature they have likes and dislikes, but I understand your point.
I expected you would, but I have a habit of saying most things on my mind.
It's fine, like I sad a peeve and a bit msleading to some.
As I said before, it's still a good story. I wait for the next chapter.
5174239
5176411
5176411
I have read this before... I just got an acc so I want you to know that I think this is a really great story and you should continue!
This has a good plot. Is this still ongoing? Cus' this is the bomb.
Please continue! I like this Fluttershy!
I'm liking this alternate universe. I would love to see what happens next.
So when's the next chapter coming out?
Will you continue this?