299709
Hmm interesting premise

Story Idea: The Anti-Conversion Equestrian Defense force (Or the "ACED force" for short.)

This would take place somewhere around the second season, or at least that would be when first contact is made

Led by Twilight Sparkle, this task force would be tasked by Celestia to hunt down an Equestrian terrorist organization operating on Earth called the PER, who have perverted Equestrian magical sciences to create a serum capable of transfiguring a human into this deranged cult's idealized conception of a pony, mind and body (and, even more worryingly, soul).

Twilight was brought onto this project for many reasons: her organizational skills; her expertise in magic of all kinds, including that which can manipulate and distort the mind, and for being the one pony Celestia can truly trust with a project of this magnitude; for her morally upstanding nature and knowledge of harmony.

Aiding her in leading this project are:

Starlight Glimmer, a unicorn with a great talent for soul magic, whose budding cult ambitions became derailed by momentous turmoil of the first contact with humanity, and who became a massive human enthusiast as a result of them being key pieces of evidence for her pet theories about the deleterious effects of cutie marks on pony society. Her rare skill in soul magic and her knowledge of the inner workings of cults make her a key resource for both the combating the PER themselves and in their efforts to counteract and reverse the effects of the serum.

Lyra Heartstrings, moderately successful musician to support herself in her true passion: cryptozoology, a field where she has become a well respected expert. She theorized the concept of a creature not unlike Man years prior to first contact, as a pet project of hers, and her work in publishing essays and creating artwork (and even works of fiction) to expound upon her theories as to how these creatures would function went a long way to bridging the gap between their societies years later when first contact would be made. She is also a highly skilled mage in the field of transfiguration of living creatures, not through any special talent, but through many years of hard work done primarily for the purpose of testing her and others' theories by creating living, breathing examples of theoretical biology (well, usually breathing, anyway.) However, more than all of this, the true reason she was brought on board to lead this organization over so many others was that it was her very research into those fields that was perverted by the PER to create their weapon. Not only does this give her a unique insight on the inner workings of the magic involved, but while she may not be as much of a passionate public advocate for humanity's greatness like Starlight and others might be, the idea of her own research being used for such vile purposes infuriates her.

Shining Armor, brother of Twilight Sparkle, leads the military divisions of organization from the front, with his skill in barrier magic saving countless humans from the ever expanding forms of serum-based weaponry that the PER employ; meanwhile Luna, a talented strategician with particular skill and experience in adapting to strange new paradigms of warfare, commands the grand strategy of their operations, as well as having a wealth of knowledge of otherwise lost magics and secrets.

And many others that I have yet to think of.

I've got bits and pieces of this story thought out already: Starlight would have occasional debates with Twilight and others about the whole "cutie mark" thing (where she would show herself to have far better reasons for disliking them in the show, with the whole "lost a friend because of his cutie mark" thing being just where she got her start, a fact which moderately embarrasses her); Twilight would learn a whole friendship lesson about her friends being able to help her in a lot of ways even when she's doing things they have no real expertise in; a group called the HLF would form, in the belief that the conversions are a plot by the Equestrian government (an understandable belief, especially when the PER have resources and information that could only have been plausibly obtained if they had key ponies in the government working with them under the table), and they become a boon and hindrance to the task force, fighting the PER's guerilla tactics with their own, but also constantly doing what they can to resist the Equestrian government, as well as the task force, who they believe to be controlled opposition.

And Lyra... oh boy, she has a doozy of a character arc.

She'd start off seeming like a mare whose interest in humans is purely scholarly, a mystery she's spent much of her time unraveling, suddenly come to life. But as the story goes on, we begin to hint at an interest that goes beyond the scholarly; she begins to gives off signs of something that might at first be respect, then admiration, then... something else. Eventually, we start to see indications that she's subtly co-opting the organization's research divisions for something. skimming resources off the top, and encouraging research tangents in directions that aren't quite in service to their goals.

Ultimately, this would culminate quite late in the story, after they finally produce a prototype of a serum that can reverse the effects of the ponification one. Soon, they are ready to announce it to the world, ready with prepared speeches for each of them and a live demonstration of the counter-serum. But soon, after the demonstration is done and the speeches are wrapping up, Lyra goes off script, a speech of her own prepared... and her own live demonstration. Lyra heartstrings consumes a different serum, one that she created in secret, and then, live in front of the world... she turns herself into a human.

For her interest in humanity had long since become an obsession, admiration turned to envy, and her skills in transfiguration had been something she developed purely as a stepping stone to this moment, where she would transcend the form she was shackled with and become a member of that species she had fallen in love with since the moment she had hypothesized their existence. Being that she's not a madpony like the PER, this serum wouldn't have the mind and soul altering properties of the other (beyond altering your motor skills and the general differences in hormones and other chemicals that affect the mind), and she's not about to force it on everyone, but she fully believes in the superiority of the human form, far more passionately and fervently than anyone else, she had just become very skilled at disguising it.

And the chapter that this happens had better be "Hey you with the pretty face", as a reference to a... relevant couple of lines from Mr. Blue Sky.