Iron Wing City.

A city of progress, a city of industry, a haven for the technologically minded. It is the pride of every griffon who lives there, and—to many—a shining beacon of griffon superiority. For the better part of three centuries, Equestria had overtaken Griffonia when it came to advances in technology, and years of civil war, bloody coups, and self-destructive avarice hadn't helped matters in the slightest.

For the longest time, Griffonia had been an empire divided and it wasn't a stretch to say that griffon society dangled on the edge of total collapse... but that all changed with the Moon Princess's betrayal of her country and Sombra's return. It wasn't the griffons themselves, but the ponies that had brought about a major change. Together, in almost no time at all, Luna and Sombra had taken control of the Crystal Empire that had mysteriously risen with the dark stallion, and—even more surprising—both had immediately declared war on Equestria.

Griffonia generally tended to keep to itself and was wont to stay out of equine affairs, but then, a few months prior to the war, Princess Luna suddenly arrived in Griffonia with a small retinue of her batpony loyalists and a few unicorns and demanded an audience with Emperor Rödrun Brave Claw IV himself. Naturally she was dismissed outright at first; her claims of the Crystal Empire's inevitable return were left unheeded and ignored, and her intent to stand with this stallion calling himself the 'king' of an 'empire' and fight against Equestria for dominance seen as laughable. It was then that she offered a gift in exchange for the Emperor's audience—the beginning move in what would later become known as the Traitor's Wager.

Intrigued, the Emperor agreed to meet with the Moon Princess and her retinue. Her 'gift'—documents containing previously undisclosed and closely guarded details of Equestrian engineering—was enough to catch the Emperor's attention, but not enough to agree to the proposed alliance between Griffonia and the Crystal Empire made by the Princess once Sombra returned. The Emperor, unconvinced of the other Empire's return, refused, stating he wouldn't meddle in pony affairs. It was then that the Traitor Princess made her 'wager'.

Griffonia could do what they pleased with the knowledge she'd given them, and Luna would even provide the services of the unicorn engineers and scientists she'd brought with her, no strings attached. If, however, Sombra and his empire returned, and he and Luna together could show that they were a dominating force against Equestria, he would agree to not only form an alliance, but help fight against the Sun Princess and her ponies. The Emperor agreed—some would've said foolishly—to the wager. Celestia and the rest of the ponies were not much loved by the Royal Family of Griffonia, and the Emperor no doubt saw this as a possible opportunity to bring the Sun Princess low.

With her task seemingly complete, the Traitor Princess returned to Equestria, leaving behind her scientists and engineers as promised. The whole affair caused the Griffonian Emperor and many of the noble families of Griffonia to stand up and take notice of events outside their lands. The Emperor was quick to put the ponies, and many of the finest minds of Griffonia to use in bringing Griffonia to new technological heights. All the while, Griffonia watched with interest as events played out, content to stay back and await the coming war. The Crystal Empire finally did appear eventually and both the Traitor Princess and King Sombra had indeed struck a quick and decisive blow against the initial advance of Equestria's forces.

The battle in the Frozen North was only a prelude to the real war to come, but that it seemed, had been enough to convince the Emperor that this alliance was worth investing in. When the Traitor Princess—now calling herself a Queen—had returned to Griffonia with news of their overwhelming victory, the accord was struck then and there, and with that, the Crystal-Griffonia Pact was formed.

The foundation had already been laid for an industrial boom in the Griffonian Empire, and the alliance had only hastened Griffonia's already impressive push towards greatness. In only a few short years, the Empire of Griffonia was launched into a new age of science and technology. With Equestria tied up in the war and fighting a desperate and ultimately futile fight against the combined forces of two Empires, technological progress proceeded unhindered, and the finest minds of Griffonia were able to not only equal Equestrian engineering, but surpass it all together.

From the stronger and faster ships of both the sky and seafaring variety and firearms to the simple creature comforts you'd now find in any griffon home, Griffonia is now more prosperous than its ever been, and nowhere is that more prevalent than Iron Wing City. Originally born from one griffon's dream of turning his small, rural hometown into a bustling city of commerce and industry, the city has grown to become one of the world's largest sources of—

A boisterous knock at the door caused one of Twilight's ears to twitch and, for the first time in roughly three hours or so, she pulled her attention away from the myriad of books she had piled up atop an already heavily cluttered desk. The desk sat near the window of a small office, which itself was on the third floor of a multistory building.

Specifically the Iron Wing City Public Archives main building.

The mare flinched violently and snapped her gaze towards the door, her amethyst eyes widening with panic and her body reacting on what had quickly become instinct over the last few days. In a flurry of unnatural motion, the unicorn had shifted into something more fitting for a resident of a heavily griffon populated metropolis.

I wonder if this is what it feels like to be a changeling?

"Who is it?" Twilight snapped in a curt and somewhat nasally feminine voice that was very much not her own, "state your name and business. I'm very busy and have no time to entertain guests at the moment."

"Aww, but I bought these super delicious cinnamon rolls from the bakery down the street that I wanted to share!" came the disappointed reply from behind the door, "are you suuure you don't have any time?"

The voice was young and bubbly, and wouldn't have sounded at all familiar to Twilight a few days ago, but she'd gotten used to it now. Even if she hadn't, the bombastic tone certainly would've given away the identity of the creature behind the voice. All the same she furrowed the brows above her half-moon spectacles and her beak turned down into a wary frown.

"...Pinkie? Is that you?"

The question was quiet and tentative, and the response was anything but. Twilight had to resist the urge to leap out of her seat as the door was thrown suddenly open. A female griffon—grey feathered, black furred, and looking just out of her fledgling years—bounced into the room with a pink paperboard box in one claw and smile as bright as the sun on her face. She opened her mouth wide as if to announce her entrance, but stopped just short, looking as though she'd forgotten something.

A second later she turned and gently shut the door behind her before whipping back around and throwing out her arms in a grand gesture. Twilight breathed a quiet sigh of relief as the black fur and grey feathers vanished beneath a tangle of black tendrils, leaving a bright pink earth pony mare beaming at her from across the room.

"Guilty as charged!" Pinkie cried happily, "heya, Twilight! How goes it?"

Satisfied that they were alone and a little annoyed at the sudden and unnecessary outburst, Twilight shed her own disguise and persona of the no-nonsense elderly griffon archivist. She hated playing the stuffy griffon, but it was something she needed to put up with for now, given her current plans. Still, she'd be lying if she said she didn't enjoy having all the knowledge of the Archives at her hooves. It certainly made things a lot easier when it came to getting information while staying undercover.

"Pinkie, you scared the hay out of me!" Twilight breathed, frowning at the pink pony, "keeping a low profile means you don't do things like that, remember?"

"Right right, sorry, Twi," Pinkie replied, though her sheepish smile lasted only an instant before her regular grin returned. She hopped over to where Twilight sat and flipped open the box before shoving it in the unicorn's face, "want a cinnamon roll? It's suuuper gooey and full of cinnamon-y goodness~"

Twilight leaned away from the box and frowned, but gave the offer some consideration. While it was true that she and her friends could no longer be called ponies or technically even living beings if her hypothesis was right, and while she had yet to find any more information on what exactly had befallen them, Twilight had found out a couple of facts. One of these facts being that, while they no long had to eat in the normal sense, they could still indulge if they wanted to, and food even still tasted the same, much to the relief of the ponies-turned-viruses.

There were other things—other benefits—to consider, but Twilight set them aside for the moment and after a few more seconds of indecision, she reached out and took a roll from the box, giving Pinkie a grateful smile in the process. She took the offered treat, if for no other reason than to remind herself of what she and the rest of her friends had been—what Twilight herself was still trying desperately to hold onto despite everything.

"Thanks, Pinkie," she finally replied before taking a bite. She took a moment, humming in appreciation at the taste, "oh wow, that is good."

"Right?" Pinkie replied, setting the box down next to one of the large stacks of books on the desk and brushing her flat raspberry mane out of her face, "I asked Fluttershy if she wanted one but..." Pinkie's smile turned sad and slightly bitter, "...she said she didn't want one... that she didn't deserve one."

There was a long, uncomfortable beat of silence between the two viruses and a moment later Twilight sighed. She placed a nearby marker in the book she'd been reading and closed it before turning her attention to the window and the bustling Griffonian city below. In some ways it reminded her of places like Manehattan and Fillydelphia, but in so many others it was completely alien to her. Some of what she and the others had seen since their arrival in Iron Wing City mirrored what she'd find in the more modernized Equestrian cities, but when it came to most things in this place, it was as if Griffonia had entered an industrial revolution completely separate from their own.

All the metal and steam, the massive walking clockwork monstrosities patrolling the streets, the ever present smell of smoke, iron and gunpowder in the air, and of course, the various self-propelled vehicles that dominated the roads and skies of the city. Griffons no longer had to rely solely on their own wing power to get around, nor did they from what Twilight could see. Most traversed the roads of the city in strange 'steam cars' or used odd mechanical flying contraptions not dissimilar to the hoof powered helicopter Pinkie had used sometimes, though no hooves or claws or paws were needed to keep this machine afloat and moving—steam did that well enough, just like with most inventions Twilight and her friends had stumbled across.

And of course, there were things like the massive airship Twilight and Rainbow had seen back at Sky Talon Labs. Twilight hadn't seen any airships in the city so far, but she knew they existed, and that they had all been made in Griffonia, including the one Twilight herself had brought down just outside the facility. Though she'd found out the origins of that giant airship, where and how that silver golem had been created was still a mystery. This city was like a testament to everything they'd all missed in the last sixteen or so years, and somewhere down there in the hustle and bustle of griffons and the odd pony or two, was Fluttershy.

Twilight had been surprised at how much the mare had changed since they'd escaped the facility. She was the same Fluttershy for the most part, but there was something else there now that hadn't been before, and it wasn't just the uncontrollable rage she experienced in combat. Looking at the city and thinking back on all of their experiences thus far, Twilight was reminded of just how much had changed during their absence.

Too much has changed... far too much.

"I told her she could wait outside the city if she wanted," Twilight muttered, more to herself than Pinkie, "I told her what we might have to do, and she chose to follow after us anyway."

"It's been four days since we got here though," Pinkie replied solemnly, moving to stare out the window along with Twilight, "do you really think she would've waited that long?"

"Honestly? I'm not sure anymore," Twilight answered with a shake of her head. She glanced up at the grey afternoon sky above the city, then turned to address Pinkie directly, "where is she now?"

"She said she was gonna take one more look around the business district, then head back to the apartment," Pinkie replied, "she said she'd wait for us there, hopefully with some good news."

Twilight nodded once, and returned her gaze to the window. It had taken some time and a bit of careful maneuvering on Twilight's part, but the three mares-turned-viruses had found a suitable arrangement that allowed them to blend in while maintaining a position in which Twilight could find out everything she needed to know about the modern world—at least where the Griffonian Empire was concerned. Twilight had found out about the old griffon archivist by chance, and, with only a bit of reluctance, had taken the opportunity presented to her.

The griffon had been part of a small family that included her husband and their granddaughter, both of whom had been dealt with and replaced by Pinkie and Fluttershy respectively. While Fluttershy had already killed several griffons during their attempted escape from Squawken, she'd never consumed a living creature until now, and the experience hadn't sat well with her—not in the slightest. Both Twilight and Pinkie knew that's why she was out there now; they knew the real reason she'd offered to scout out the town and seek information on her own was so that she could ruminate on what she'd done.

"So... did you find out anything useful?" Pinkie tried, attempting to break the melancholy quiet of the room.

"I did actually," Twilight answered, giving a small nod, but not looking in Pinkie's direction, "I found a few books on microbiology, but oddly enough, not much on virology specifically. Even if I had found more in the field of virology, I don't think it would've helped much anyway, given the circumstances of how this virus was created," she frowned and glanced back at Pinkie, "I tried comparing what I found to the notes you took from the facility, but the information doesn't match up all that well, if at all."

"Wait, so if you didn't find anything out about the virus, then what did you find?" Pinkie asked with a bemused frown.

"Something that might potentially be much better," Twilight answered, fully turning to face Pinkie with a small smile of triumph—a smile that vanished into a concerned frown as she continued, "it was heavily restricted, but I managed to get the information on where Sky Talon Labs is located."

"Sky Talon Labs?" Pinkie asked, her bemused frown turning thoughtful. Recognition suddenly crossed her face and she gasped loudly a moment later, "isn't that the name of the place where we—"

"Yes, Pinkie," Twilight hissed, "it is, and I think it'd be best for us if you didn't go shouting out details best left unheard by anypo... anyone that might be listening in. Low. Profile."

"Right, sorry again," Pinkie apologized distractedly. Giving Twilight a worried look, she spoke again, albeit in a much quieter tone, "but how is finding out where we were being held better than..." she trailed off and this time a look of realization crossed her face, "....oooohhh."

"Exactly," Twilight answered, grabbing another cinnamon roll from the box and biting into it. She paused a moment to swallow the food and continued, "there's are a couple of things I figured out from my research, but nothing concrete just yet, and I'd rather not go into detail until we meet back up with Fluttershy, but as much as I don't want to, I'm willing to bet there's still a lot we can learn from that place if we go back."

Pinkie bit her lip and looked away, lost in thought. Twilight watched her as she quietly took another bite of the roll, waiting for her reaction. It was clear she was having reservations about going back to the place they'd just barely managed to escape from, and Twilight had no doubt Fluttershy would have something to say about it. If Twilight was being honest, she didn't really feel good about going back either, but she felt this was their best bet—not only in possibly stopping the potential outbreak at the source, but also in finding out just what this had all been about.

After all, Isn't this why they'd all decided to stay behind while the others had left for Equestria?

Pinkie seemed to realize this, because a few seconds later she gave a slow nod that picked up pace with her confidence.

"Yeah, I guess you're right, Twi," the pink mare conceded. Twilight could still see some hesitation in her smile, but she was still on board. The unicorn's relieved smile dipped a bit as Pinkie's own smile disappeared, "I agree, it's probably the best start we're gonna get, but I also have a reeeaallly bad feeling something not-so-good is gonna happen if we go," before Twilight could reply, Pinkie held up her hooves, "I'm still with you, though, Twilight—one hundred percent... and I'm sure Fluttershy is too, or will be once you tell her."

Twilight noted the uncertainty in Pinkie's voice at that last part and her frown deepened. She looked down at the partially eaten cinnamon roll in her hoof and gave another, longer sigh.

"I hope you're right, Pinkie," Twilight muttered morosely, "because as much as I hate it, this is the only lead we've got right now."

Pinkie looked at Twilight; she took in her lost expression and—with pangs of guilt, sorrow, and longing—wondered not for the first time since they'd reached Iron Wing City how Rainbow, Rarity and Applejack were faring. She wondered if they'd already reached Equestria and what they'd find there. She wondered about her other friends and family back home and whether or not they'd survived the last sixteen years.

So much time had passed and so many changes had befallen the world that she wondered if Equestria could even be saved.

Author's Notes:

I felt I started The Viruses of Harmony without a proper foundation for the events that took place 16 years prior to the story, and I aim to fix that in the third 'book' of this tale, so expect me to throw in some lore (and possibly flashback chapters, as much as I hate them) every now and then between other stuff that goes on in the story.

I also plan on branching out in this one, so no more entire arcs taking place in one... place, as it were. One last note is that I'll probably be keeping the chapters a bit shorter (generally between 2k and 3k words long) in an effort to keep updates a little more quick and consistent. All that aside though, hope you guys enjoy!