One of the enemies of Equestria, now reformed, Discord could change the playing board at a moment’s notice if he so wished. Discord lacked any actual concern with Equestrian politics and had the power to become the biggest threat to all of Equestria, all he needed was to get bored or annoyed enough to make it happen. So, both the Loyalists and the Regent began to create Anti-Discord initiatives, and they both came to the same conclusions; whoever controlled Fluttershy controlled Discord.
And so, many tried to appease Fluttershy. The quiet little mare found herself being the most important pony in all of Equestria, receiving generous gifts and funding for her animal sanctuary from groups who made their affiliations known to her, and all the while she was spied on by both factions.
One day, Rarity and the Regent both found Discord in their offices. He smiled to both of them, and gave them both the same bone chilling message.
“If either of you so much as touches Fluttershy, I will turn Equestria into a chaotic hellscape the likes of which you cannot even imagine. Up will be down, black will be white, dogs and cats will live together in perfect harmony, and each of you will fondly remember the days when all you had to worry about was a civil war.
Fluttershy no longer received gifts or bribes or even so much as a note in the mail. Indeed, it is believed for a time, Fluttershy seemed to be the only pony the war did not effect. But in secret, the factions, for the first time, had an agreement; Discord had to die.
One day, while Fluttershy was visiting her friend, two small armies of ponies attacked the small dimensionally unstable cottage Discord called home. Discord was confident he could erase them with ease, but was surprised to find that Rarity was among them – and she had the Alicorn Amulet.
“That might be a problem.”
Both Armies were quick to assault the house, each fearing the others’ intentions might have been to capture Discord by force. Discord only paid attention to Rarity, feeling she was clearly the most obvious threat, and indeed she had somehow managed to enchant the clothing her soldiers wore to protect them from his chaos magic. He threw everything he had at them, from flying pigs to kick me signs that compelled ponies who saw them to kick the wearer, but Rarity undid every spell. Discord was certain that as long as she had that amulet, this particular battle with her could go on for years with neither of them coming out ahead. Discord was stronger, but Rarity was clever, and that made her dangerous.
Little did he know that while he had his back turned, the Regent’s ponies attempted to capture Fluttershy. The mare screamed out loud as soldiers attacked her and grabbed at her, and Discord’s attention was diverted for just an instant. Long enough for Rarity to hurl a few enchanted spears at him, wounding him with magic that made it difficult for him to heal as quickly as he might otherwise do.
Fluttershy, seeing Discord hurt, became desperate, and grabbed one of the soldiers’ weapons and began swinging it wildly as she made her way to Discord.
Then she fell was a spear flew through the air and pinned her into the dirt.
Everything seemed to pause. Rarity’s eyes widened in horror. Discord turned to her, his eyes wide. Rarity struggled with words, uttering out silently.
“This wasn’t supposed to happen.”
Discord reached forward and grabbed the amulet around her neck. The magic that bound it to her unraveled instantly as he pulled it off like cheap jewelry and broke it in his claws. In an instant, he slithered to Fluttershy, and held her close. She stared at him with fear in her eyes, gasping for air.
And in the next istant, both were gone. The house was gone. The area was a simple, grass field, where two small armies who hated each other stood.
Both feared Discord would return, and so both did not bother fighting each other. They fled. Many did not even return to their masters and left Equestria altogether.
Years later, Rarity had received reports of the Regent’s men attacking one of her safe houses. She had ponies working hard to find out how they had learned of that safe house, and how many others were at risk. She made her way to her office to have a seat and a glass of something strong, and when she opened the door, somepony was in her seat.
Rarity almost shouted.
“Please don’t scream,” said the gentle voice of an old friend, “I don’t think you’d like what would happen if you screamed. I’m still kind of getting used to what I can do, and I don’t want to cause too much trouble.”
Fluttershy smiled. “Oh, you do remember me? I was afraid the fur, the lions’ paws, the goat hooves, and the antlers would throw you off. I know, I know, it’s strange fashion, but I find that works for me these days.”
Rarity tried to speak, but no words came out.
“Surprised to see me? I guess I would be too, what with the spear that went through my chest.” She looked up as Rarity struggled with more words. “Oh, yeah, about that? Kind of related to my new look. You see, as I lay there, dying from a spear in my chest - I would not recommend that particular fashion choice - Discord took me somewhere safe. Discord’s power has limits, and sadly healing a mortal wound is not his specialty. So, he did the only thing he could do and gave me his power.”
Rarity seemed shocked. “D-Discord… sacrificed himself to save you?”
Fluttershy giggled a disturbingly innocent sounding giggle. “Yes, it was awful sweet of him. Now, he’s a part of me, and I have to be honest, sometimes it’s difficult for me to tell where he ends and I begin.” Fluttershy’s smile broadened. “Hey, do you like trees?”
Before Rarity could answer, Fluttershy snapped her claws, and in an instant, foliage erupted from the ground beneath her as a tree sprouted to full size, destroying much of the mansion. Rarity fled outside and looked up at the massive tree that had grown from the middle of her home, announcing her presence to the world in a not-so-subtle way. Fluttershy was gone, but she had made her point, and as Rarity looked around, she could already see crowds gathering to figure out what had just happened.
Another safe house compromised. Rarity fled without a word.
The Everfree Wild is an odd faction formed by those who fled the war that had erupted in Equestria. Once a bunch of wanderers who avoided cities, they had been brought together by Fluttershy. Unlike the other warring factions whose goals are to establish themselves as the seats of power, Fluttershy’s goal is to end the civil war by any means necessary – even if that involves destroying all the other factions. In her belief, after that, either Equestria will sort itself out, or it will crumble. They tend to attack with large numbers of animals, magical plants, and their particular methods often destroy entire towns with rapidly formed forests which, themselves, resemble things from the Everfree - earning them the title “Everfree Zones.”
Fluttershy herself seems to have been changed by Discord’s power, having inherited some of his own personality traits, though often putting her own spin on him. Fluttershy revels in the chaos that is inherent in nature, and places she has gained a foothold in tend to be filled with plant-life and animals. She has built her fortress in the Everfree Forest, which has become more dangerous as she has begun to pour her own newfound powers into it.
Her second in command is Zecora, who believes that Fluttershy is so much more than even she realizes; the Zebra mare believes Fluttershy, through the power she gained from Discord, maybe the new leader Equestria needs, and that she could build an empire more powerful and prosperous than even that left by the Royal Sisters. Still, Fluttershy is a dear friend, and she does not try to force her to this, though she makes no secret of her views.
The faction itself has many ponies of all races who have built their houses in the trees of the forest. Many of them have studied in natural magic, and have even learned a thing or two about Fluttershy’s own powers. Within their ranks, many are sorcerers, beast-masters, and rangers, skilled in jungle warfare, and often so in sync with Fluttershy herself that they seem unfazed anytime she makes particular changes to the battlefield.