> Retexo
>  by Xz Hacker
> --------------------------------------------------------------------------

> Chapter One: “Settling Down”
> --------------------------------------------------------------------------

{Authors Notes: Please read part one of this story before reading this as you will be extremely confused if you don't. This is a direct continuation of my story Commutatus, (Link) but the writing style and mood is significantly different enough to warrant uploading them as separate stories. I apologize for any confusion or inconvenience caused by this.}

Chapter One: “Settling Down”
One month had passed since Applejack the alicorn, and all of her friends and family had moved to Canterlot, but to Applejack it seemed only a matter of days. The activity had been almost nonstop, and she had barely anytime to herself. Rainbow Dash was always wanting to compare flight maneuvers and their potential speed. Twilight was always asking for help on incredibly complicated spells. Pinky Pie was as usual always trying to throw a party for someone or something. Rarity was off in her own fantasy, living her dream. Fluttershy was always attending to the animals in the royal garden, as they had finally warmed up to her. The Cutie Mark Crusaders had been up to all kinds of mischief, but hadn't seriously hurt anyone, other than themselves, yet. Celestia seemed a considerable deal more relaxed having Applejack under such close supervision, but Luna seemed to want nothing more than to speak at length with Applejack about philosophy and her opinions on the order of things.
During all the madness of settling in, Applejack found herself more and more grateful for her ability to fly, and after the first two weeks, teleport. (A trick she finally asked Twilight about.) Applejack had begun to fly, or teleport, to the top of the castle regularly to escape the constant madness  that was everyone settling in. At first it was merely to escape, but it had slowly began to be about the air and looking at the sky, day or night.
One night she was looking at the stars when Luna spotted her and flew up to talk. “Sister, are you enjoying the night sky,” Luna asked merrily, as she approached Applejack on the castle's roof and landed.
“Yeah, it's nice to look at you know?”
“Indeed, we have spent many a night staring off into the endlessness of space. That was part of the reason we once were so angry with our subjects, as it seemed as if none of them appreciated the beauty of our night sky. We are glad to see you find it as charming as us.”
Applejack turned her gaze slowly from the night sky to Luna, “Luna, tell me, how does Celestia really feel about me?”
Luna stared for a moment, she had not expected such a direct question. Their relationship had evolved quite rapidly over the last month, and most of the formality Applejack had held was gone, but the forwardness of the question startled Luna. “Well, we, uh.”
Applejack turned her head back to the sky, “it's fine Luna, ah shouldn'ta asked you that, I'm sorry.”
Luna shook her head, “No no, we are sorry, it's just,” she stared for a moment, “our sister has been very on edge about this situation. We feel like she is merely worried for the sake of her subjects, and wishes to protect them from any harm.”
Applejack looked back at Luna curiously, “ah promised no more Rainbooms, ah have Twilight's help in figuring out mah magic, ah don't aim to hurt no one, why does Celestia think I mean any harm?”
Luna looked empathetic, “It is not that sister believes you to be a direct threat, but you need to realize the implications of thine state. You are the first of your kind, you became like us, something no one has ever done before, this may herald a new age, and with change comes strife. Sister merely wants to manage whatever may come of your condition.”
“What could happen, ah mean, you don't plan to use the elements on any one else to do this to them do ya?”
“Never,” Luna snapped, appalled by the idea, but she immediately lightened up again, “we would never intentionally force someone into a burden such as this.”
Applejack still didn't understand what could possibly happen that would cause anyone harm. Luna bid Applejack farewell and continued on her nightly patrol, while Applejack stayed staring at the night sky.
The next morning Applejack found herself facing down Twilight, Dr. Patella, and a very large syringe. Applejack moved back away from them, “why the hay do you need mah blood?”
Twilight moved slowly forward, “come on AJ, you know we are only trying to help you, we just need to make sure you are well, and blood work is standard procedure.”
“Ah feel fine,” Applejack protested, as she backed up to the wall of her bedroom.
“I know, but we need to make sure you're alright,” Twilight said as she inched forward with the syringe hovering slightly in front of her.
“Ah'm warning you, stay back!”
Twilight lunged with the syringe and found herself stabbing it into the wall moments after Applejack teleported away.
“Now what,” Dr. Patella asked annoyed.
Twilight closed her eyes for a moment, then teleported to the roof next to Applejack. She yelled “got ya,” and lunged once more, this time Applejack jumped away and began to backwing away from Twilight.
Applejack laughed a little, “try and get me now.”
Twilight got an angry look and began to say something when she lost her footing and began to slip, she yelled a little as she began to fall. Applejack, never missing a beat, swooped down and grabbed her mid fall. They slowly made there way to the ground and Applejack, still holding Twilight, looked down and asked, “you alright sugar cube?”
Twilight looked up at her said “thanks AJ.”
Applejack smiled, “no problem Twi...” she was interrupted by a sharp sting in her leg she was holding Twilight with, and Twilight yelling “gotcha!”
“Ow,” Applejack protested as she dropped Twilight to the ground.
“Don't be a baby,” Twilight said as she smiled and looked at the small, but more than sufficient blood sample she had just collected.
“Ah hate needles,” Applejack said vehemently as she rubbed her arm.
The rest of the day went smoothly, and without anymore needles.
The next day Dr. Patella asked Applejack and the Princesses to meet her in private.
Dr. Patella looked around nervously as the three Alicorns walked into the room. She saw the guards following them in and got wide eyed. “What are they doing? They need to leave, this is very important, only you can hear.”
Taken aback at the severity of her tone, and the almost paranoid look in her eyes, Celestia hesitantly nodded for the guards to leave, and they proceeded to leave the four alone in the throne room.
Looking around for anymore intruders, Dr. Patella slowly grew ever so slightly more relaxed upon seeing they seemed alone. She looked up at them and took a deep breath before beginning. “Yesterday I obtained a blood sample from Applejack here,” Applejack glared angrily at the word obtained. Unfazed Dr. Patella continued, “at first I was just going to merely run standard tests, just see if she was healthy, then I got curious as to how her DNA compared to that of normal Ponies, so I started taking a close look. Well at first I was stunned to see what I saw, but well, it was incredible.”
Celestia was looking uneasy about this, “Doctor please, the point?”
Dr. Patella seemed to snap back from the awe of whatever she had seen. “Yes of course, where was I? Right, looking at her DNA through incredibly powerful magnification devices, I noticed a rather peculiar thing. Her DNA was that of your average Earth Pony, however there were small molecules attached to her DNA that seems to be the cause of her,” Dr. Patella paused, she was hesitant to use the only word she knew to describe Applejack's condition, “erm... mutation.”
Celestia seemed annoyed, “Doctor I fail to see why this is of so much importance. How does it affect the situation any?”
Dr. Patella looked quite frustrated with her lack of understanding, “these molecules, they are somewhat viral, they cause this mutation, and cause the body to begin replicating these molecules, that's why Applejack's changes quickened in pace.”
Celestia looked panicked, “VIRAL,” she yelled, “you mean others could get it?!”
Dr. Patella got pale, and shushed her, “Please princess, calm down.”
Celestia settled down a bit. But Luna was beginning to get worried as well, “Doctor we need to know, do you mean to say it is contagious?”
Dr. Patella frowned, “not like a cold, no, however contact with her blood may cause the same reaction to take place in anyone.”
Luna looked gravely at Applejack, “and you are absolutely sure of this fact?”
Dr. Patella shook her head, “no, I did drop a bit of my blood into a batch of hers to see if the molecules would bond, they seemed to take to my blood as well as hers, however, I'm no virologist. I cannot be entirely sure if the Alicorn effect can be replicated, or even if the C1 molecules are actually responsible for her change.”
Applejack looked questioningly at Dr. Patella, “C1?”
“My apologies, that is the abbreviation of the name I have given these molecules, Commutatus one molecules.”
Ignoring the conversation about the names of the molecules in question Celestia interrupted, “how can we make sure of what you believe?”
Dr. Patella once again looked incredibly paranoid, “princess with all due respect, I don't think anyone should be told about this, this could be very very dangerous.”
Celestia glared, “I am quite aware of that, but that is the very reason why we must understand what we are dealing with, no Doctor I will not ask again, how can we be sure?”
“Well there are two options, the first is to out right test our hypothesis, and inject a small amount of Applejack's blood into someone,” Celestia glared disapprovingly, “or... we could get a virologist to take a look at what we have found.”
Celestia looked extremely displeased, “there are no other options?”
“I'm sorry princess, I simply do not have the knowledge to adequately assess the affects and the contagiousness of C1.”
Celestia looked around at everyone, “until we can render a decision, I want no one to tell a soul about what was discussed here today, my sister and I will decide on what to do shortly, until then,” she looked at Dr. Patella, “you keep that blood sample locked up and secure while,” she turned to Applejack, “you do your best to avoid any injury.”
> Chapter Two: “The Debates”
> --------------------------------------------------------------------------

Chapter Two: “The Debates”
After Dr. Patella had left, Luna was the first to speak, “sister,” she said looking at Celestia, “we think it would only be fair to have Applejack take part in these deliberations.”
Celestia stared at Luna for a moment, then looked towards Applejack, and sighed, “very well, but let us get to work immediately, action needs to be taken.”
Luna nodded in agreement, “indeed we find this development as disturbing as thou dear sister, and what do thou think dear Applejack?”
Applejack shook her head, “ah'm not quite sure what to make of it honestly, I don't think it would be a good idea to just out right test her theory on someone, but...” Applejack trailed off.
Celestia nodded, seemingly in agreement, “yes, we can't have anyone else go through the change, but we need some way to be sure of this C1's affects, and just how contagious it may be.”
Luna ventured a solution, “it sounded as if Dr. Patella knew that a virologist could easily tell what this substance did, as well as if it could spread, why do we not simply take it to one?”
Celestia looked at her sister, “no, no, who knows what an outsider could do with information like this, it's a wonder that Patella didn't inject herself with the substance to test it. Can you imagine the mayhem if this got out of hoof?”
Celestia was loosing her normal cool again, and Luna was seeing her sisters point. Applejack decided to state the obvious, “but what other choice do we got? There ain't any other way to test if C1 is the cause of my condition.”
Celestia and Luna both looked at her, Celestia nodded and said, “you may be right, although I still don't like it. I'm afraid this may get out of hand if not properly controlled. I don't need to tell you how much devastation someone with our power can cause.”
Luna and Applejack nodded in agreement, Applejack perked up, “well what if me and Twilight just watched what the virologist did, and ,made sure he didn't do nuthin funny?”
Celestia eyed Applejack, “you may be on to something, however I know you do not know enough to adequately monitor the work, and I'm not sure if Twilight does.”
Luna chimed in, “we know that Twilight is trustworthy. We think it would be a good idea to inform her of the situation, and ask if she believes she is up to the task.”
Celestia nodded, “yes that sounds like a plan.” She walked over to the door and opened it, “guards please locate Twilight and tell her she is urgently needed in the throne room.”
The guards sought out Twilight and told her she was needed in the throne room, she rushed there, and was briefly described the situation and asked if she believed she was able to oversee the examination of the C1.
“To be honest princess I'm not entirely sure. I know some about viruses and their replication, but as far as determining how they affect living matter, I don't think I'm educated nearly enough to handle this.”
Celestia looked grim, “I was afraid of that, it appears we have no choice but to trust an outsider with this information. However I still wish you would oversee the research Twilight, as it may discourage any ill intentions that may arise if the virologist believes he is being supervised.”
Twilight nodded, “of course, I'll do my best princess.”
“I know you will, and thank you.”
Luna then asked, “sister have you forgotten of the previous sample already taken?”
Celestia shook her head, “no, that will not be an issue, Twilight and Applejack will get that from Dr. Patella, and will deliver to whomever she believes to be the most suitable candidate for its analysis. Hopefully we can avoid mentioning were the blood came from, and what we believe it to do. Twilight, please do not mention to anyone what C1 is, or how we believe it to work, even the virologist that Dr. Patella sends you to. It is of the utmost importance that no one is aware of this. If the virologist inquires as to the origin, inform him that that information is under royal protection. Also inform Dr. Patella I wish for her to supervise the analysis with you, and of the secrecy that must be maintained.”
Twilight, though worried about the extreme precautions Celestia was implementing, said, “you can count on me.”
Applejack and Twilight then set off to Dr. Patellas office, not very far from the castle. Once inside they explained the entire situation and what they had been ordered to do. Dr. Patella looked incredibly worried, “oh this is bad, I don't think this is a good idea.”
Twilight looked at her sternly, “It doesn't matter, we have been ordered to do this, we need to get this C1 analyzed immediately.”
“There isn't a single member of the scientific community I trust, and Commutatus one is extremely dangerous.”
Applejack stepped forward, “we know that, but this is the best solution me and the princesses could come up with, there is no other way.”
“OK, OK,” Dr. Patella said as she slowly walked to a safe. She opened it and pulled out a small vile of blood. “This is all of the sample I have left, I used most of it on standard tests, but this should be more than enough. I suppose if we seriously need someone else for this, then the only person I could think of is Dr. Aden, although that guy creeps me out.”
“Where does he work,” Twilight asked.
Dr. Patella took Twilight and Applejack to Dr. Aden's office. Once inside they began to speak with the virologist.
“Doctor, we are here on royal business, it is of the utmost urgency you analyze the compound that has been mixed in with this blood sample,” Twilight said as she levitated the vile to the small male Unicorn, with a brown coat, dark brown mane, and a cutie mark that appeared to be a dark ball with protrusions.
Dr. Aden frowned and telepathically held the vile in front of him, “and what pray tell am I to be analyzing  it for,” he asked with an irritating, and irritated tone.
Dr. Patella stepped up, “I recently came across a substance I have dubbed Commutatus one or C1. It appears to be viral in nature, and by royal order we need you to look at it and determine its affects and whether or not you think it is contagious in any way. We will be supervising your work as this is of high importance and urgency.”
Even more annoyed, he looked at Dr. Patella with disdain, “I'm sorry did you say supervise? Are any of you actually qualified to work with my equipment, or in my field of research?”
Getting quite irritated herself Applejack looked him strait in the eyes and angrily said, “look are you going to help us or not?”
Straightening up a bit at getting stared down by an angry alicorn he said, “of course I will help, just try and stay out of my way.”
He began his work almost immediately, looking at the blood sample through a magnification device. He stared at the C1 for several hours until finally he said, “this C1 as you call it seems to be nothing more than a common cold variant that is slightly aggressive.”
“Ah haven't felt sick,” Applejack said a little suspiciously.
Twilight shot Applejack a look, as Applejack just gave away the origin of the sample.
“Of course not,” Dr. Aden said, completely ignoring the look Twilight had given Applejack, as he threw the slide that was holding the blood sample he had been viewing in the trash, “ever since the elements transformed you into an alicorn, I'd be surprised to learn you were ever sick. Each type of pony has a natural resistance to the effects of certain types of illness. Earth ponies have a natural tolerance to anything that heavily affects the stomach or liver, Pegasus have a high tolerance to any heat or cold related illness, such as the common cold, or the flu. Finally, Unicorns have a tendency to not catch anything that would affect their concentration, such as anything that would cause them to be tired. Alicorns on the other hand benefit from all these natural resistances, and then some. Old studies done on the princesses back when they were more curious about their own physiology indicated that they were almost impervious to illness, and in most cases injury.”
Applejack was still stuck on how he knew about the elements turning her into an alicorn. “How'd you know about the elements and all that?”
“Please, as if the entire scientific community wasn't in an uproar over you, no one was spared Patella's 'I found the first pony to become an alicorn' speech.”
Applejack and Twilight turned and stared at Dr. Patella, who sheepishly bowed her head, “well... it was the find of the century, and that WAS before I was told not to tell any one by Celestia.”
Dr. Aden levitated the vile to Twilight, “you can have that back it is worthless, I suppose you should burn it if you are worried about any one catching that strain of the cold, as it does seem aggressive, but it should be out of her system in a month or two, assuming that her system even bothers fighting it.”
Dr. Patella looked simultaneously relieved and disappointed at this news. Twilight and Applejack seemed satisfied that the situation was resolved, and went back to the castle to report the news to Celestia. She seemed relieved to here the news, and agreed to the destroying of the blood sample.
> Chapter Three: “C2”
> --------------------------------------------------------------------------

Chapter Three: “C2”
Several months later Dr. Patella came back to ask Applejack for another blood sample.
“Ah don't want to get stuck with a needle again. Aden said that it was nothing, and it would be gone by now.”
“I'm aware, I just can't help but shake the feeling he missed something.”
“Isn't he an expert or something?”
“Please Applejack, I'm only curious.”
“Fine, but this is the last time you get any of my blood.”
Dr. Patella withdrew a sizable amount of blood from Applejack, half because she knew that the alicorn was serious about not letting her get more, and half out of spite for making it so difficult to obtain in the first place.
Dr. Patella went to her lab and looked at some of the sample with a magnification device. She quickly saw that it appeared nothing had changed from the last sample. The same amount of C1 still persisted. Worried, she quickly got Twilight and brought her to her lab.
“What do you make of it Twilight?”
Twilight stared for a long time, not needing to see the image for that long, but needing time to process its implications. “Well doctor, I must say this is unnerving, it appears Dr. Aden was mistaken about C1, as it certainly hasn't gone away as he predicted.”
“Yes, and it appears to not even have decreased in its amount, I'm afraid we may need to confront him with this.”
“First we must speak with Celestia.”
“You go handle that with the princess, I'll go talk with Aden, and get his opinion on this development, then I'll meet you at the castle.”
Twilight went immediately to the castle and sought out Celestia. Celestia listened to what Twilight had to say with careful attention and worry. “Oh my, that is troubling, you said that Patella was going to fetch Aden?”
“I believe so, or at least tell him what we have learned, and ask him his opinion.”
Just then Dr. Patella bolted into the room with a panicked look on her face, “princess terrible news, Dr. Aden has disappeared.”
Celestia looked relatively calm, “how long has he been missing?”
“By the sounds of things, everyone agrees he just left several months ago, right after we visited him with the sample.”
Still calm Celestia ventured, “this must be a coincidence, we destroyed the sample he was using, and he can't possibly replicate C1, could he?”
Dr. Patella settled down a bit, “no, it's nearly impossible to replicate a virus by hand, especially without a model to compare it to, replicating it from memory is unthinkable, he would have to have a sample to work with.”
Twilight jumped a little at a though that had just occurred to her, “Patella, what about the sample he actually had on the slide, what happened to that?”
Dr. Patella's eyes got wide, “we left that with him, he threw it in the trash, he must have taken it back out and took it with him.”
Celestia was looking nervous, but made an attempt to restore calm, “now let us not jump to conclusions, there is still all the possibility that this is merely a coincidence, and that C1 is nothing more than a strong cold virus.”
Dr. Patella looked skeptical, “regardless we need his help with this, if hes not up to no good somewhere, we still need to bring him in to take a second look.”
Celestia nodded, “your right, I'll have the guards on lookout for him, and send an investigation team to try and find him. I'm sure he could not have simply disappeared, surely someone knows where he has gone.”
The next day the guards reported that there were no leads as to the current whereabouts of Dr. Aden, nor any clue as to what prompted his leave. It appeared that no one knew when, where to, or why Dr. Aden had left. Celestia was getting nervous. “I want all guards across Equestria on alert, we need to find him.”
Twilight was worried about the princess. “Princess are you OK, I mean this isn't that big of a problem yet, is it?”
Celestia looked dark, “I'm not sure my student, things seem to have gotten out of hand somewhere along the line, and I need to get things straightened out. Somewhere out there is a doctor that may or may not have a chemical that can turn ponies into alicorns.
Twilight knew she was partially to blame for the sample getting left behind and questioned no further.
In the meantime, Dr. Patella was busily working and reading up on viruses, attempting to see if she could possibly understand anything more about C1. After several hours of work, Twilight came to help. They both spent the next several days analyzing data and reading everything they could get there hoofs on related to viruses.
After much work, the two had finally come to a conclusion. They decided that it was time to speak with Celestia about what they had found. Twilight entered Celestia's chamber followed closely by Dr. Patella. Celestia turned her attention away from a letter she was reading to greet them. “Yes Twilight, what is it?”
Twilight got straight to the point, “for the last several days Dr. Patella and I have been studying the C1 compound and reading up on virology, we have come to three distinct conclusions. The first is that C1 is most definitely the cause of Applejack's becoming an alicorn, two, that there is no possible way that Dr. Aden could have mistaken C1 for a cold virus, and three, that C1 will only affect Applejack's physiology due to the unique way it reacts with DNA.”
Celestia thought for a moment, “so if I understand properly, Dr. Aden knew that C1 caused Applejack to become an alicorn, which is why he took a sample and disappeared, but it can't be used to turn anyone but Applejack into an alicorn?”
Dr. Patella stepped forward, “correct, except for one minor potential issue. There is a distinct possibility that Aden is planing to reverse engineer C1, and attempt to make it work on himself, or others.”
Celestia nodded, “that would explain this,” she said as she levitated the letter she had been reading over to Twilight.

Dear Princess Celestia,

I'm sorry to bother you princess, but you ordered us to report any unusual activity. Recently we came across multiple Pegasus, who claimed that a week prior they had been Earth Ponies. Upon interrogation, and further investigation it appeared that all three were telling the truth, and that other than their new wings, they were the exact same as a week prior.

Reporting from Fillydelphia North Post
Captain R.J.T.

Seeing she was done reading Celestia began talking, “go fetch Applejack, you two and her will need to go the Fillydelphia, and investigate these cases.”
“ME,” Dr. Patella asked, not quite yelling, but not quite staying quiet.
Twilight turned to her, “doctor, you know more about ponies becoming alicorns then anyone else at this point. We will need you.”
Dr. Patella didn't look happy, but she nodded regardless.
Twilight and Dr. Patella went and got Applejack and explained what they had found, and what Celestia had shown them in the letter from Fillydelphia. When they were finished explaining, the three of them went straight to the train station. The train took them directly to  Fillydelphia where they went to the nearby royal guard station to speak with the three, now Pegasus Ponies.
They where all in an interrogation room, although none of them looked entirely uneasy. When Applejack, Twilight, and Dr. Patella walked in, one of them did not hesitate to make his feelings known. “Hey,” he yelled, “I don't know who you think you are keeping us here like this, we ain't done nothing wrong.” The ponies wings were open backward, something that tended to happen to Pegasus  when they were angry.
The other two nodded in agreement but didn't speak. Twilight attempted to calm the angry pony down. “I'm sorry for any inconvenience sir, it's just that you're particular situation is of interest to princess Celestia, and we have been sent to investigate what is happening here.”
The angry pony cocked his head slightly, looking first at Twilight, then at Applejack, and finally at Dr. Patella before he spoke again. “You three don't seem like guard, we have already answered a hundred and one questions, what more do you want from us.”
Dr. Patella pulled out three syringes, “actually blood samples, I need to test your blood for C1.”
“C1 whats that,” the male asked as Twilight shot Dr. Patella a look. Twilight shook her head and answered, “I'm sorry that information is protected by royal decree.”
The man grumbled slightly and then held out his leg, “make it quick.” The two females followed his lead and held out their legs as well.
When Dr. Patella withdrew his blood he winced slightly. Applejack noticed and asked “are you OK?”
He smiled and laughed slightly, “can't be as bad as these stupid wings coming in, hurt like you wouldn't believe.” The two females mumbled in agreement. Applejack nodded, “you don't need to tell me, they hurt me somethin fierce too.”
The man once again cocked his head and looked at Applejack curiously, “you mean you had some of whatever this stuff the docs testing for and it gave you wings too? Where you a Unicorn?”
Twilight jumped between them, “I'm sorry that information is...” Twilight was interrupted by Applejack putting her hoof in front of Twilight's mouth. “Now hold on a sec sugar cube, he deserves the truth, I was a normal Earth Pony, then the stuff she's testing for turned me into this. Some fella named Dr. Aden took some of my blood, and we think he is tryin to use it ta turn ponies or himself into alicorns like me.”
“I appreciate the honesty, all right you scratched my back, I'll scratch yours. The guy who gave us this stuff didn't go by Dr. Aden, said he was Dr. Nade.”
Twilight almost laughed, “hes using an anagram, that's a little cliche.”
The man continued, “he told us that he could fix us up with a new drug he was testing, said he could fix my back aches, told those two it would help them with their acne.” The two shy teenagers nodded.
Dr. Patella finished drawing the blood from the last of them and looked up, “got a little more than you bargained for by the sounds of it.”
“Your telling me, these things hurt a lot, took a full week to come in.”
“A week,” Dr. Patella asked curiously, “Twilight, how long after initial healing did it take Applejack to develop first signs of wings?”
Twilight stopped and thought for a moment, “over two weeks for certain, wouldn't you say Applejack.”
“Sounds bout right,” Applejack said, not actually giving it much thought.
Dr. Patella thought deeply for several seconds, “well there is no way to tell what to do without analyzing these blood samples, so I'll head off to the nearby hospital. This city's big enough to have a lab there.”
Twilight nodded, “I'll join you.” They both began walking out when Twilight noticed Applejack wasn't following, “Applejack are you coming?”
Applejack shook her head, “you two go on, I'ma stay here and help these three with their new wings, ah'm the only one who knows what they are going through. It would only be right to help them figure this out.”
Twilight didn't look very happy with the idea, but nodded and said, “alright, we will be back as soon as we are finished at the lab, don't wander off. This will only take a few hours at the most.”
Applejack then spent the next few hours teaching the new Pegasus about how to control their wings, how to fly in general, and even managed to show them a few tips on how to increase speed she picked up from Rainbow Dash before Twilight and Dr. Patella came back.
Twilight looked worried, and as soon as she saw Applejack, began to inform her of why, “Oh this is bad, we looked at those samples and found that Aden has been doing some serious work at unraveling how they work. Other than being Earth Ponies, those three had nearly nothing in common with you. He managed to isolate the part of C1 that gave you wings, an make it affect any Earth Pony.”
Dr. Patella stepped in, “on top of that, this C2 seems to be almost triple the speed of C1.”
Applejack and Twilight stared, Dr. Patella looked at them for a second before realizing why they were staring, “what, it only makes sense to call it C2.”
Twilight sighed, “there isn't anything we can do here. The guards have already looked in all the areas Dr. 'Nade' was reported being in, so for now we will just have to report back to Celestia what we found and wait for the night.”
“We can't go back to Canterlot,” Dr. Patella asked almost whining.
Twilight shook her head, “I'm afraid not,  Fillydelphia is closer to most other major cities, and we know that wherever Dr. Aden went it was from here, so we need to stay here until we can find where to go to next. Celestia has already prepared us a place to stay at a nearby hotel in case we could not find any immediate leads to go on. W'e will stay there until Celestia says otherwise.”
Dr. Patella's head drooped, “fine...”
> Chapter Four: “Epidemic”
> --------------------------------------------------------------------------

Chapter Four: “Epidemic”
Three days passed, and no word had come about Dr. Aden's potential whereabouts. During that time the combined efforts of Twilight and Dr. Patella led to the creation of Retexo one, or R1, a compound designed to neutralize the contagious C2. R1 was administered to all three of Dr. Aden's victims in  Fillydelphia, however the physical alterations were irreversible. Shortly thereafter Twilight, Dr. Patella, and Applejack returned to Canterlot.
After three weeks Dr. Patella returned to her normal practice, and Twilight kept studying virology, having found a legitimate interest in it. Applejack still couldn't stop thinking about Dr. Aden and where he could be. Applejack was on the castle's roof again one evening when Pinkie Pie crept up on her. “Hey AJ whatcha doing?”
Applejack nearly jumped off the roof, her wings halfway outstretched ready to attempt to fly away. When she saw it was just Pinkie Pie she settled back down, “jeez Pinkie, you liked ta scared me right off the roof.”
“Oopsie, sorry AJ, still though, watcha doin?”
“Nothing really, just siting up here enjoying the view.”
By this time word had gotten around to all her friends about what was happening, Pinkie Pie being no exception, and seeing the look on Applejack's face Pinkie Pie knew Applejack was thinking about it, “it's not your fault you know.”
Applejack turned to look at her, “but it is, if I didn't let myself get hurt when we were fightin Discord none of this woulda ever happened.”
“What if I had gotten hurt, or Rainbow Dash, what if we needed healing, would it be our fault?”
Applejack looked back at the sky, “I know what your trying to say Pinkie, its just hard to think about, somepony could be getting hurt right now because of me.”
“Then help everyone you can until you can fix this problem.”
“What can I do?”
“Your an alicorn,” Pinkie Pie stood up and gave Applejack a hug, “I'm sure you can think of something.”
Pinkie Pie left Applejack alone on the roof once more. After a few minutes Twilight teleported  beside her, “AJ it's time to go, they think they've found Aden. It seems he made his way to Los Pegasus. The guards are waiting for us before they begin the raid on his compound.”
Applejack nodded, “we don't have time to loose, where is Patella?”
“At her office why...”
Applejack didn't wait for Twilight to finish, she grabbed her and teleported to Dr. Patella's office. Dr. Patella was shocked for a second, but Applejack gave her no time to think. She grabbed her as well and teleported the three of them to Celestia's throne room, “Celestia, ah've never been to Los Pegasus, can ya get us there?”
Celestia didn't hesitate, “of course.” She walked over, touched Applejack's shoulder, and they all three found themselves in the busy and bright streets of Los Pegasus.
Dr. Patella yelled, “what's going on?!”
Twilight turned to her, “we found Dr. Aden, his facility is here in Los Pegasus.”
“That's half way across Equestria!”
Applejack was ignoring their conversation, “Twilight where is his compound?”
Twilight pulled out a piece of paper and gave the address, they all ran towards the building. Once they got there, they found several royal guards waiting for them.
Twilight walked right up to the commanding officer, “are you sure Dr. Aden is in there?”
“We were following up on several missing persons reports. During a stakeout one of my boys noticed your Dr. Aden, and recognized him from his description in the all point bulletin out on him.”
“Right, we will follow you in. Don't touch any of the equipment or anything suspicious looking, your job is to apprehend Dr. Aden, is that clear?”
The guard made a quick wave to his seven men that were with him, “men we are under strict orders to avoid tampering with any equipment or anything else we find inside,  we are only to do what is necessary to apprehend Dr. Aden, is that clear?”
All the other guards said “yes sir” simultaneously.
They all approached the main door to the building and prepared to breach it. The commanding officer looked around at his men, “on three, ready, one, two, THREE!”
They busted down the door and they all stormed in at once. Dr. Aden was no more than fifteen feet away from the door, and as soon as they came in, he bolted into another room. “Alpha team, after him!” Four of his seven men took off chasing him, the other three stayed behind to secure the room for Twilight, Applejack, and Dr. Patella.
The room they were in was full of equipment. The tables were filled with multiple batches of  Commutatus variants in air tight capsules. There were also several doors with viewing plates which also seemed to be air tight. Twilight noticed a small notebook and walked over and began reading it.
One of the guards walked over and peered into one of the doors. Twilight beckoned Dr. Patella and Applejack over to the table were she was reading. “It seems that Dr. Aden has been working on  Commutatus quite heavily, it seems that its been taken to the sixth generation already. This journal actual keeps, well, disturbing amounts of detail on his trial and error with the virus.”
Dr. Patella peered at the book, “yes but will any of it help us reverse engineer the current version, that should be our top priority.”
While they were speaking, the guard that had been peering into one of the air tight rooms realized that there was a pony inside. He began to open the door to let the captive out. When Twilight heard the airlock depressurize she yelled, “NO WAIT!”
It was to late, from inside the room stepped out a deformed looking alicorn, with a small horn, and wings that dwarfed Applejack's. The pony slowly walked towards the guard that had let her out, and reached out and touched him. He fell on the ground writhing in pain. Twilight grabbed the journal, Applejack, and Dr. Patella and teleported them outside the building. She began to talk frantically, “we need to get out of hear RIGHT NOW!”
Applejack looked confused, “what about Dr. Aden?”
“He doesn't matter as much as getting out of the city immediately, we need to get back to Celestia, we need to quarantine the city.”
Dr. Patella looked livid, “you don't mean that C6 is...”
Twilight finished her statement for her, “it's highly contagious by mere touch, it causes mutations in minutes, and is highly unstable. Worse yet, it tends to cause brain damage.”
Just then the guards that had been with them in the room began running out of the building yelling, as both the alicorn released from the air tight room and the guard she had touched, who now seemed to have grown small wings and had his horn enlarged significantly, came slowly walking out behind them.
Twilight turned to look at them for a moment then yelled, “Applejack, get us out of here!”
Applejack grabbed them both and teleported them back to the roof of the castle in Canterlot, then to the throne room in front of Celestia, where Twilight began at an unbelievable pace, “Princess we need to quarantine Los Pegasus immediately. Commutatus six has been released and its is unbelievably contagious. We must stop the spread before it becomes a pandemic.”
Celestia blinked then said, “I'll fetch your brother, hes the only one who can do this.”
Twilight stared for a moment, “your going to magically seal off the whole city? I meant...”
“Is it dangerous?”
“Yes”
“Then having your brother seal the city is the only way to protect my subjects.”
Celestia then teleported off to get Shining Armour. Once she found him, she quickly explained to him the situation, and teleported him to the outskirts of Los Pegasus, where he began to seal the entire city in.
Back at Canterlot, Twilight was still trying to get her head around what was happening, “she's going to use my brother to quarantine the entire city. There gonna seal off an entire city like...”
Twilight trailed off for a moment, and Applejack finished the thought, “like a giant tomb.”
> Chapter Five: “C7 and R2”
> --------------------------------------------------------------------------

Chapter Five: “C7 and R2”
Reports were pouring in about the tragedy that was the Los Pegasus outbreak, and talks of survivors making there way to the outer edges of the quarantine zone, only to find themselves trapped by Shining Armour's protection spell.
With the aid of Dr. Aden's research notes, Twilight and Dr. Patella had been actively working on Retexo two, in an attempt to reverse the affects of C6, and C7, which they learned from reading was perfected mere days before the raid on Dr. Aden's compound in Los Pegasus.
Celestia made it a point to read the entire journal, and learn everything she could about Dr. Aden and his research. Celestia had just finished reading the notes on the test subject used for C7 and had a few questions for Twilight, “Twilight you have read all this, yes?”
Twilight barely turning from her work said, “yes princess.”
“If I understood this correctly, the C7 compound will turn anyone into an alicorn, and is nearly as contagious as C6?”
Twilight turned, “that's about right, except it doesn't work hardly as fast, it seems that his test subject for C7 took three full days to develop wings, and to grow to full size. He also did us the favor of documenting how fast it becomes contagious, it seems that C7 will not spread until several days after the full development of the alicorn, but it seems to become airborne at that time.”
Celestia looked grim, “so how long do we have before Dr. Aden begins to spread C7, assuming he has already injected himself?”
Twilight looked confused, “princess, you don't honestly think he made it out of the city before my brother's spell sealed it do you?”
Celestia nodded, “it's true we sealed the city in a matter of minutes, but if he ran straight for the outskirts of the city, there is every possibility he made it out.”
Dr. Patella decided to look up from her work to speak, “it's fine, me and Twilight are already working on R2. Thanks to the doctor's meticulous diagrams and research notes, we should be able to counteract C7 in no time at all.”
Celestia stared at Dr. Patella intensely, “how long is no time at all?”
Dr. Patella straightened up a bit, “um... well, by the looks of things, no more than three days.”
Celestia bowed her head, “not enough time to stop Dr. Aden from becoming an alicorn.”
Twilight looked confident, “don't worry princess, from what we are reading, C6 and C7 work a lot differently than C2, we are almost positive that all physical side affects of any of the Commutatus compounds can be reversed except for C2 and C3, both of which have been destroyed by Dr. Aden, and the only known test cases were given R1.”
Celestia bid them luck on their work and went to find Applejack. As usual, she found her on the roof. Celestia walked up and sat down beside her. “You know you will need to be the one to face him,” she said bluntly.
Applejack looked up, “I had planned to, why wouldn't I?”
Celestia shook her head, “I mean that you won't have Twilight or Patella there to help you when we find him, because there is a chance he will be contagious. We don't know how the compound will affect Luna or myself, but we know that any Commutatus compound will render the others inert, meaning you will be immune to C7.”
Applejack had not yet thought of that, “I... have to face him alone.”
Celestia nodded solemnly, “yes, I wish there was another way, but...”
Applejack stood up, “No, ah understand, it needs to be me.”
Four more days passed and Twilight and Dr. Patella were just finishing work on R2 when the reports came in. Several ponies in Baltimare had fallen ill, and were reporting pains in there sides and foreheads, after reportedly seeing a male alicorn walking through the city. Celestia lost no time rounding everyone up. In the throne room she began strategizing for the upcoming encounter, “all right how has your development of R2 come along?”
Twilight looked confident, “it is completed, we need to get to a larger laboratory to mass produce it if we want to clear out Los Pegasus, but we can get that done in a matter of hours with the right equipment.”
Celestia nodded, “good but our target isn't Los Pegasus, your brother still has that well contained, we can fix that later. Right now our concern is stopping the C7 outbreak that seems to be occurring in Baltimare. You two will begin mass production of R2, we will need a lot of it. In the mean time, Applejack, you need to go and keep Dr. Aden busy, he needs to  be stopped. We can't let him get away, I'll bring the Wonder Bolts, and once Twilight and Dr. Patella have finished production we will dump the R2 over Baltimare.”
They all agreed on this plan. Twilight and Dr. Patella ran straight for the largest lab in Canterlot. Applejack was transported to Baltimare, while Celestia went to go and inform the Wonder Bolts of their mission.
Applejack was all alone for the first time in a while. She had escaped to the roof of the castle often in an attempt to get some privacy from the chaos that was her family and friends adjusting to their new life in Canterlot, but now more than ever, she wished they were all here to help her through this.
Applejack made her way to the nearby hospital, where she knew the patients who had reported seeing Dr. Aden would be. Once inside, she asked several of them what they had seen, and where they had seen him. All of them gave the the exact same description of a large alicorn, with huge wings, taller than Applejack, with the same brown coat and dark brown mane. They each said they saw him walking through the streets downtown, appearing to be in no hurry, or to be going in any particular direction. She got the names of the streets they had seen him on, and then set out to find Dr. Aden.
She wasn't flying around very long before she found him, slowly walking down the streets. He had become taller than Applejack, and his wings did seem larger. He saw her shadow pass over head, he looked up in time to see her drop in front of him. “Ah, my dear Applejack, so nice to see you, how have you been?” Dr. Aden seemed unusually calm and happy to see her.
Ignoring his tone Applejack snapped, “the jig is up Aden, ah'm taking you in.”
Dr. Aden got an angry look, but then his face relaxed a bit and he smiled, “taking me in, for what, what have I done?”
“You've purposely infected ponies with a virus, you're hurting innocent people!”
“HURTING?!” Dr. Aden began to laugh, “my dear girl that couldn't be farther from the truth,” he said in harsh tones. “I'm helping these people. I'm giving Pegasus the magic that they were jealous of from the old time, giving Earth Ponies the wings that they had so envied, and making all the races able to resist any disease, and live essentially forever.”
Applejack's eyes narrowed, “Is that what ya did for the ponies of Los Pegasus?”
Dr. Aden grew even angrier, “what happened in Los Pegasus was not my fault! You and your idiot friends released C6-TS3, not me!”
Applejack faltered for a moment then stood tall again, “and did that pony volunteer for your experiments doctor? The guards said they were investigating several missing persons reports when they found you.”
Dr. Aden took a step back and got a defensive tone, “I was trying to help people, I needed someone to test on, I...”
Applejack didn't let him finish, “ya kidnapped several ponies to fulfill your own selfish desires!”
Dr. Aden took a step back towards her, putting them inches apart, yelling, “SELFISH, I have worked hard for the last few months to give everyone everlasting life, and you have the audacity to call ME selfish, look at yourself, you and the princesses are guilty of hoarding immortality to yourselves!”
“Ah didn't ask to be this way!”
“You can't tell me that you don't want to live forever,” Dr. Aden said slyly, regaining some of his previous cool.
Applejack hung her head, “actually, ah don't, I just wanted to be normal, ah just wanna be left alone on mah farm, left in peace from all this.”
Dr. Aden stared at her for a moment in stunned silence, “you must be a fool,” he finally said. “Fear of death is all that keeps people going in life, how could you possibly not want immortality?”
Applejack looked up defiantly, “cause I don't live because ah fear death, I live cause I have the love of my friends and family, cause they need me and ah need them!”
Dr. Aden took another step back, “that's... ridiculous, people don't really care for each other, we all just attracted out of our nature. There is no such thing as love or caring for one another.”
Applejack took a step forward, “then why are you trying to give immortality to these ponies? Ain't that against your nature, to help others?”
Dr. Aden set there in stunned silence once more, confronted with the contradictions in his motives, he was unsure of what to do.
Applejack saw the confusion in his eyes and thought she had swayed him, “come back to Canterlot with me, Twi can help undo what you did ta yourself.”
Dr. Aden jerked out of his trance, “NO,” he yelled backing away, “you can't have my immortality, it's mine.” With the last word he began to blast Applejack with a powerful spell. Applejack reflexively threw up a magical defense which seemed to hold. After a few seconds, Dr. Aden threw even more effort into it. Applejack tried to hold her own, but seemed weaker than Dr. Aden. After three more seconds she lost her focus and Dr. Aden's blast hit her full force. She went rocketing towards a nearby building and made a large hole in the wall.
Applejack slowly stood up and looked over at Dr. Aden, who was barely panting from that powerful blast. She knew he had almost a lifetime's worth of experience using magic over her, and that she couldn't possibly beat him going toe to toe.
Dr. Aden smiled, “go home Applejack, you can't beat me. I'm far superior in magical strength than you!”
Applejack knew he was right, however she also knew that he didn't have nearly as much experience with his new wings as she did. So she kicked off into the air and began to circle over head. She fired a burst of magic straight at him, which he deflected, however once he looked back up, he was surprised to see Applejack flying straight at him. He barely had time to yell before she slammed into him. They began to wrestle, also something Applejack had a considerable deal more experience with. After a few seconds of grappling she managed to position herself on top of him, where she hooked both her forelegs underneath his wings and on top of his neck, in a hold that only worked on Pegasus.
Dr. Aden attempted to buck her off, but Applejack just tightened up, hurting his wings, which Applejack knew were more sensitive then Pegasus normally let on. After a moment he began trying to cast a spell. When Applejack noticed, she cranked on the hold she had him in. He yelled out in pain and fell to his knees. They stayed like that for several seconds, panting until Applejack finally spoke, “now will ya calm down and listen to me for a sec?”
Dr. Aden struggled once more before settling down and said, “what more is there to say, I don't want your 'help' and there's nothing you can say that will change my mind.”
“The princesses may let ya keep your immortality, but we can't have you going around forcing it on other ponies.”
“Bah, lies, the princesses would never let me keep my immortality, not after everything that has happened.”
“Ya don't know that, at least talk with 'em. They would listen to ya if you just surrendered rather than going around causing all these problems.”
Dr. Aden sighed, “maybe your right, maybe if I would have just talked with them in the first place they could have seen things my way, but its far too late for that now, they won't forgive me for what I've done.”
“Its not too late to undo the damage.”
“What do you mean, I have infected hundreds of ponies with the virus, there is no possible way to contain them all now. What could you possibly do, seal this city too?”
Applejack looked off into the distance and saw a formation of Pegasi headed to the city carrying a large container. She smiled and let go of Dr. Aden and pointed up at the Wonder Bolts coming in, “no we are gonna cure 'em!”
The Wonder Bolts reached the edge of the city and turned on the large container which began to sprinkle out the mist of R2. Dr. Aden stared at the Wonder Bolts as they passed over head, and then the cloud of clear mist that descended upon them. “What is that?”
“The cure for C6 and C7.”
“Cure...” Dr. Aden said unsure, and seemingly tired, he swayed a little and fell over. Applejack looked down at him, everything seemed to be getting fuzzy. The R2 seemed to be affecting her much the same way as it was affecting him. She took a step towards him and then collapsed, unable to hold herself up. She stared up after the Wonder Bolts spraying the city, then slowly closed her eyes, and then all went black.
> Chapter Six: “Undone”
> --------------------------------------------------------------------------

Chapter Six: “Undone”
Applejack slowly opened her eyes to find Twilight with her back turned to her, and Rainbow Dash grinning. Rainbow Dash nearly jumped up when she saw Applejack open her eyes, “Hey Twilight AJ's awake!”
Twilight turned around smiling, “Applejack! How are you feeling,” she asked, quickly walking to her side.
Applejack slowly sat up and looked around. They appeared to be in a hospital room, but it was quite large and seemed to be private. “Where am I,” she asked sleepily.
Twilight answered, “this is the private medical wing in the Castle.”
“What happened,” Applejack asked, slowly remembering the last things that had happened to her.
Twilight explained, “well, we covered Baltimare in Retexo two, and it seemed to counteract the affects of C7 almost entirely. When the search teams went in, they found you and Dr. Aden near the middle of the city passed out. We took you both back to Canterlot. After three days Aden had reverted back to a Unicorn, and well...”
Rainbow Dash took the initiative and said, “you've been passed out for two weeks, and your a normal Earth Pony again.”
Twilight shot Rainbow Dash a look, but Applejack was too stunned to notice. She got up out of bed and stood there for a moment before saying, “let me see.”
Twilight went out and grabbed a mirror from a nearby room and brought it back. She levitated it in front of Applejack, who sat there for a moment focusing on it, before realizing she no longer had the magic necessary to telepathically grab things. She reached out and took the mirror and began studying herself. She looked exactly as she had before, except her hair was still as long as it was when she was an alicorn. She was the same height as before, and she no longer had a horn or wings. She stayed looking in the mirror for several minutes, before finally speaking. “Well, I s'pose that this is what I wanted.”
Twilight could see the pain in her eyes, “we could always try to find some C1 and...”
Applejack held up her hoof to stop her, “it's fine Twi, ah just need some time to get used to things again.”
For the next several months Applejack got used to being an Earth Pony again. When she inquired into the fate of Dr. Aden, she was informed he was sentenced to a lifetime in the castle's dungeon. After she seemed back to her normal self mentally, not just physically, Celestia asked if she wanted to move back to Sweet Apple Acres. After much consideration she decided it would be best. Her and all her friends and family then moved back to Ponyville, and returned to what half a year prior had been normal life. All they had to show for their adventure was a grand tale of good intentions gone wrong.
> Epilogue: “Shared Fate”
> --------------------------------------------------------------------------

Over three hundred years later Celestia walked into the dungeon beneath the Canterlot castle. She slowly made her way to the cell that so long ago Dr. Aden had been sentenced to a lifetime of imprisonment. She stared into the cell with cold eyes and after a moment spoke. “Aden, you have a visitor.”
Inside the cell Dr. Aden sat, looking no more different than the day he had first been put in this cell, but still somehow anyone could sense how old he was by the look in his eyes. He slowly looked up and met Celestia's cold gaze with eyes that would make anyone who had not lived for at least several hundred years shudder, and said “who could possibly want to see little old me?”
Just then Applejack walked in behind Celestia, looking just the same as she had when he had seen her last, over two hundred years ago. Her eyes, like his, told a story of old age, despite her youthful face. “We need your help, otherwise we wouldn't have come, Aden.”
He could hear the difference three hundred years had made in her voice, “call me doctor.”


{Authors Notes: I would once again like to thank my friends John, Cody, Craig, and Chris for helping with spell and grammar check, also my grandmother for helping me put the finishing touches. I would also like to especially thank Chris for challenging  me to write this. Finally I would like to thank the community for all they have done for me. A few quick things: 1. Yes that is the end and I plan to write no further into the time line of this story, 2. I do however plan to make two side stories related to Retexo, 3. These side stories names will be “Dr. Aden's Research Notes,” and “C7-TS1”}