@Align  
Eh, it was either that or Fluttershy joining the guard with RD, Being ambushed in the battle that took RD’s wing and becoming so mentally damaged at what she saw that she was discharged from service. And now to pay for food she works on Sweet Apple Acres shearing sheep… But that just didn’t seem to like a good story. So I went with the long elaborate plot.

@Outcast’s Redeemer  
Overall good and sad, but you did play the “she’s adopted so it’s not creepy” trope completely straight.

@ArrJaySketch  
Well I have a theory… Now granted we only see one glimpse of her but that glimpse tells a whole lot. That said most of this is MY OWN BS so it may seem a little out there.
 
Now let’s start at the beginning of this storyline. Fluttershy is a weak flyer with height meaning she is trapped on the ground until she can become a stronger one or somepony tries to find her. But nopony dose. Instead nopony notices that she is missing until her parents come to pick her up months later.(Little) Macintosh, Seeing as the flight camp is somewhere near the farm, finds and takes her home to wait for somepony to come pick her up. Nopony comes. Due to something, be it natural or unnatural, takes Fluttershy’s parents from the world before they could be reunited. Fluttershy thinking that her parents forgot about her began to slip into depression. Mac takes charge and tries to figure out where her parents were and learns what has happened. Following his botched attempt at gently telling her that she now an orphan, Macintosh decides to help her overcome the grief of being alone and convinces his grandmother to adopt her. Fluttershy, now officially an apple by law, cuts herself away from anypony besides Macintosh, Granny smith and Baby Applebloom. Fluttershy gradually comes out of her shell as she helps (Medium) Mac with farm chores. Fluttershy, due to her work on the farm and with the animals, gains her cutie mark of three butterflies. But due to the work she does has her hair kept short. Years pass and the two ponies grew closer and closer, cementing their sibling/best friend type bond.(think Kim Possible and ron stoppable friendship.) Fluttershy grows enough that she starts to feel that she must take on a new challenge. But before she could try and find a suitable home to try and live on her own the events of all the main villains would occur, only more violent. A few months before the Empire would return, Big Mac, pressured by the demand for food for Celestia’s growing guard, would open the west orchard. After a month of hard labor and heartache the farm starts to show profits. Fluttershy felt that it wasn’t the right time to leave her home settled on living in a different house on the property. She takes the job of animal caretaker so that Big Macintosh can focus on the tasking work of running a farm. They would grow closer to the point that they start to feel something more for each other… But before they could explore those new feelings The Empire returned and with it war. Burdened by the new pressure of converting his farm to a machine of war, the loss of many of his cousins, uncles, and friends to the fight against Sombra’s army, and the pressure of now having to care for his new god daughter Diamond Tiara, his baby sister Apple Bloom, as well as his other sister who returned with one of his younger cousin both in depressed states due to them losing Both Aunt and Uncle Orange and the young cousins’ sister, he begins to seclude himself from everything that could wait including a relationship. Fluttershy would try to take pressure off of him, but due to her own work load, is also under large amounts of stress. It would only increase as both struggled to keep with the demands of war.
 
what do ya think ArrJay? Think any of that fits?

Alternately, Mayor Mare now has a long flowing mane like Fluttershy Prime.

@youregoingtoloveme  
That’s the spirit! X3

I want to draw more of Fluttershy like this. It’s just sort of sad. I like to imagine she had a long mane and tail right up until the War…

@PacificGreen  
“We can do it! _{Um, that is, if that’s okay with you.}”

@Outcast’s Redeemer  
Lack of fanart shouldn’t just be not allowed. It should be…
 

 
Huehue.
 
Anyways, yeah, someone should do a Fluttershy the Riveter thing.

@PacificGreen
 
I Agree the lack of fan art is something that must not be allowed. I’m thinking a rosie the riveter poster starring Fluttershy as Rosie… Imagine that poster. “If She can do it so can you!”

Why have I seen no art of Fluttershy sporting this style?

I just noticed something, She’s near the Apple Farm… THE FLUTTERMAC SAILS ON!

@Background Pony Number 17  
Perhaps she is the gatherer of all animal and not-quite-animal by-products and resources that assist in the war effort. Wool, milk, eggs, honey, etc.  
Perhaps if she knew that she could communicate with animals on a different level, she could convince the odd Ursa Major to join the fight against Sombra’s forces.

@Background Pony Number 17  

@youregoingtoloveme  
I always figured cattle and sheep were the “serfs” of Equestria. They’re not full citizens, and are confined to Earth pony farms where they trade their milk and wool for three hots and a cot and protection from the odd roaming monster.
 
Also, I just noticed in this pic that Fluttershy is doing the sheep-shearing. Even without the Rainboom, she apparently had some connection with animals.

@wselfwulf  
G.I.Shy: A Real Equestrian Hero.

@adatron  
Or it was a mandatory crew cut

With this kind of work, long hair would get in the way. She’d probably cut it by mistake.

Looks like mane & tail extensions are a luxury one can’t afford in wartime
 
She’ll never know what happened to the Tiny Ewes

And hey, I’m blind. I posted my previous comment not long after waking up and I now see that Shy’s jumpsuit accommodates her wings just fine.
 
Sheep are most likely independent contractors when it comes to peddling their wool. They are most likely organizing a union for higher wages, better treatment, retirement benefits, and all that. Penning them seems antiquated and speciesist.

@youregoingtoloveme  
But doesn’t her suit have wing holes?

@Krek  
Well the sheep CAN speak. We saw that in Sisterhooves social episode. Though that was ALSO immediately after Applejack and Applebloom herded them into a pen so… [Shrug]

In this alternate timeline (hell, even in the show itself), are the sheep basically just like livestock with basic animal intelligence, or are they on the same level of ponies here and are volunteers?

@youregoingtoloveme  
*Fluttershears

Two-thirds of the pony tribes don’t have wings but that’s no reason why Fluttersheer can’t have a government issue jumpsuit with wingholes. That looks very uncomfortable.  
War is hell.