The Alicorn Project

by Bry7x7x7

Rating: teen
Tags: Alternate Universe, Science Fiction
Length: 5205

Not all ponies adore the princesses. Some wish to find others to worship.

Princess Celestia, Luna, Cadance, and Twilight are the only known alicorns in all of Equestria. All are worshiped and loved by all.

Well, not by all. Some question their rule and seek challengers to the throne. A number of scientists, volunteers, and wealthy financial supporters came together to create their vision. This was known as 'The Alicorn Project.'

Published 1970-01-01 00:00:00 UTC
Last updated 2015-10-05 16:06:33 UTC

Prologue Part One: The Project

For a thousand years, Equestria been under Princess Celestia's rule. Her sister, Princess Luna, has also returned to co-rule by her side. Her niece, Princess Cadance, takes care of The Crystal Empire. Princess Twilight Sparkle also plays a hoof in the politics and the well being of Equestria. They are loved and worshiped all over the land. They are figures that demand respect.

Not all the ponies respect them though. There're those who question the princesses capabilities. Sure the sisters defeated Discord, but they question why they nearly lost to him hardly a year ago. He might be reformed now, but in a delicate way. He sided with Lord Tirek and his apology was a bouquet of flowers! After that he let his anger get the hold of him and almost sent somepony to another dimension, at The Grand Galloping Gala no less!

Nightmare Moon was defeated, but for how long? She could come back. Can Luna and her sister control her? The elements are gone. Speaking of, the elements were able to make her normal, but Celestia banished her. She never gave an explanation to her choice. Some ponies discredit the choice all together.

Princess Cadance was captured by the changeling queen, Chrysalis. The changelings almost took over Canterlot by tearing it down from the inside and nopony was the wiser. Celestia lost in her duel with Chrysalis. Luna was nowhere to be found and never knew much about the incident. Twilight may not have been a princess at the time, but she and her friends failed to reach the elements. Canterlot was saved by sheer luck. Not only was the pony that should have noticed kept his position as captain of the guard, but is now also the consort title holder as prince of The Crystal Empire!

Cadance was worked to near exhaustion trying to repel King Sombra from The Empire. Twilight was almost stopped by the most "threatening" obstacle of them all, stairs. Sure there was the door that showed your greatest fear and the trap at the top, but it's the stairs that everypony focuses on once they hear it.

The sisters were captured by vines of all things. Their absence caused fear and panic. The Everfree Forest almost escaped from its confinements and spread over Equestria. The elements were then lost in the process.

Lord Tirek got Discord to betray his so called friends. Although everypony can agree that Tirek was a special case, some argue that if there were more alicorns to respond to him in his weaker state instead of somepony as untrustworthy as Discord, disaster would have been avoided.

Twilight almost fell to a cult that could have taken over. She had to be rescued by common ponies. The princess of friendship needed to be saved by a group of normal ponies! An almighty alicorn was left helpless by a simple unicorn! If only Equestria was better equipped to handle what should have been a meaningless task.

With all the power an alicorn has, there were instances in which if other alicorns existed, the situation would have ended up much better than it did. All these facts settled in some ponies and they now want to enact change. So some nobles came together to fund a project. The Alicorn Project. Some of Equestria's greatest minds joined the project and gathered a number of volunteers. Each has their own reasoning to be here. Some wish to dethrone the sisters, others want more alicorn protectors. Most ponies used to worship the goddess "Lauren Faust," the creator, but in recent times, it's believed that Faust had abandoned them. So now they worship a pantheon of gods. The project's members pledge their allegiance and prayers to the god of alicorns, "M.A. Larson."

From all corners of Equestria did the project search. It searched for members, albet in secrecy. It also searched for artifacts. items that can hold the power that they need. At points, it was best to pay experienced explorers to hunt high and low for such items. Sometimes, they needed to be stolen from museums or private collections. Others were near suicidal to gather.

Another thing the project searched was whatever was left over from Starswirl The Bearded. The project's first set goal was to replicate the spell that turned Twilight into an alicorn princess. They don't have access to the spell so they have to build from the ground up to recreate the spell. They need to find as much of his research and maybe combine them with the artifacts they recover.

A problem quickly plagued the project from its foundation. There's little research from Starswirl that they can find that the public can get access to. The rest of it are closely guarded secrets for the power that the wrong hooves can do with them. To try to take that research will blow the project wide open. There's almost no artifacts that are of any use the project and its goals.

After countless study, the project was almost canceled due to the inability to replicate the spell that turned Twilight into an alicorn. Having almost crashed and burned, the project was on its death bed until a scientist suggested that perhaps they can find a gene in pony DNA that might make an alicorn.

The scientist reasoned that since there is a gene in pony DNA that decides what kind of pony that they would be (earth pony, unicorn, pegasus, or even bat pony) there can be a gene that will make an alicorn. It was possible, but it's hard to say whether or not that it's the case for the alicorn princesses aren't known for having romantic relationships with other ponies and therefore have not reproduced to prove whether or not alicorns can exist naturally through something like genetics. The Alicorn Project was in desperate need though.

The new plan was to gather DNA samples from the four princesses to locate the supposed gene to synthetically create alicorns. The nobles continued their funding and everypony prayed to Larson. The project then showed signs of life.

Prologue Part Two: The Magic Gene

The Alicorn Project was saved from certain death. It then moved its focus from magical transformation to synthetic genetic replication and engineering. The original idea was to try to clone the princesses, but most of the nobles funding the project found it morally detestable. They refused to fund the cloning project and insisted on an alternative. After discussing the other options with the scientists, they proposed that take DNA samples from the princesses and isolate the supposed alicorn gene and try to replicate it.

Once the gene is replicated, they'll introduce it into an egg cell. The nobles proposed that the project tries a charitable approach. The project will find mares that have romantic partners and wish to have foals, but have deficient ovaries and are unable to produce egg cells. They'll make a synthetic egg cell from the mare's DNA and will introduce the mare's romantic partner's sperm cells to the egg, effectively making the couple's own foal. Then the scientists will put the alicorn gene in place of the other pony (earth, pegasus, unicorn) gene and pray to Larson that the mare becomes pregnant with the new alicorn.

Some of the scientists argued that the process is overly complicated and runs a high risk of failure. For starters, the couple must have a barren mare that has a fertile partner and must not have any genetic diseases. The couple must also be willing to keep the secret and to top it off, be in favor of the project's cause. Isolating the possible alicorn gene is much more work than simply replicating the entire genome. The pony genome has yet to be fully mapped and it's still one of the biggest ongoing research fields in biology. Without such a map, locating an alicorn gene, if it exists, can take months if not years. Then there's creating a synthetic egg cell. Most genetic engineering involves a natural egg cell. The technology just simply wasn't there yet.

However, if the project was to continue receive funding, those were the conditions they must abide by. They did strike a bit of luck when they managed to find fifty couples that fit. That was of course fifty more than they thought they can get to volunteer. To find the gene that determines the kind pony, they collected DNA from the volunteers and their colleagues. They scanned the entire genome to locate what each of the genes each kind of pony share each other. The hope was that the gene is in the same place on the chromosome so when looking at the princesses DNA, they would find the alicorn gene much easier, if it exists.

They did find the gene on the same chromosome in a couple months. On a side note, they found that the earth pony trait is dominant to the others, followed by the unicorn trait by observing that earth ponies having the gene for earth pony on one of their alleles and one of kinds of pony on the other allele. The pegasus trait is recessive to each of them. Due to its rarity, it can be assumed that the bat pony trait is recessive to the others, but the scientists were unable to study that. If the alicorn gene is real, it's unknown whether or not the trait is dominant or recessive, but both of the donated alleles will be modified to have the gene to make up both alleles.

With that figured out, the scientists needed to create synthetic egg cells. They decided to try to speed up the process with magic. They figured that since they're working with phospholipids and proteins to make the cell structure rather than delicate DNA, they believed that they can work with such small material with their magic. Once they created the structure to the cell, they put the separated allele from the mare volunteers into the artificial nucleus. It took several tries, but they finally came up with a working gamete cell. Once they get the alicorn gene, they'll then introduce the partner's sperm and inject the alicorn gene into the alleles to alter the chromosome.

The plan was set. First, the scientists needed a DNA sample from each of the princesses. The most obvious way to collect their sample is hair. The ponies they hired to steal artifacts from museums or private collections were hired again to take hair from Twilight and Cadance's mane brushes, but Celestia and Luna have an unusual kind of mane. It's believed that their manes never need to be brushed and don't shed off. It's best to gather samples from all four princesses to help with the isolating the gene.

So the scientists needed something else. They went with the next best thing, feathers. They knew that the princesses molt their feathers as pegisi do. The molted feathers are swept up by the cleaning staff at the castle and burned as an easy way to rid of them. So all they needed was to get the feathers from a maid. Something a bag of bits handled quite well.

With hair and feather samples from the four princesses, they were scanned for the gene that they should have that nopony else should have. Twilight's DNA came up as a normal unicorn's, but that was attributed to the fact she was magically transformed into her form. The other three did have an unrecognized gene in place of the other observed ponies. The alicorn gene was real and thank Larson they had found it.

More synthetic egg cells were made. They were then fertilized and the copies of the alicorn gene was inserted into them. Each of the fifty volunteer mares were inseminated. The scientists knew that only a few would result pregnancy. The rest would either be rejected by the mare's body or fail to implant itself to the uterine walls. The hope was that at least one would succeed, but they needed to wait for more than twenty four hours to check to see if it was worth it.

Present Day: The Results

Creamy Caramel is one of the mares that volunteered to attempt to become pregnant with one of the alicorn foals. Yesterday, she was inseminated with the fertilized egg and is now in an examination room being looked over by a doctor to see if she had successfully become pregnant. She's lying on her back on a medical exam table with a screening crystal mounted above her. The crystal scans a section of her belly and displays an image in front of the doctor. It gives the doctor a precise look into her body to see what's going on. If she's pregnant, the doctor will be able to see the blastocyst implanted to her uterine wall.

The doctor continued to observe the displayed image. Caramel's husband, Brown Caramel, is sitting next to her and holding her hoof. The doctor has told them not to get too excited, because there's already been twenty failed tests before her, but not to lose hope.

Sweat is dripping from both of their foreheads and Brown is holding Creamy's hoof rather tightly. They were told that if they didn't become parents, they would be given a thousand bits and must keep The Alicorn Project a secret. As good as a thousand bits are, they may not get to have such a close chance to parenthood again. They are in deep prayer as firm believers in the goddess "Meghan McCarthy," the most accepted to be the head of the pantheon of gods as well as a link to the fabled human world which Twilight has been to on a few occasions.

The doctor then started to write something down and called in another doctor. The Caramels held their breaths.

"Larson smiles upon you." the doctor said, "May I be the first to congratulate you Mr. and Miss. Caramel on the successful pregnancy."

Smiles plastered on their faces, The Caramels let their breaths out in sharp, excited gasps.

"We did check the sex chromosomes before hoof and I'm proud to say that, in eleven months, you'll be the parents of a happy little colt."

The Caramels simply embraced each other while they held back the tears.

"The doctor I just called in is going to come in here and look it over to make sure everything is fine and then he'll talk to you about your accommodations here at the facility."

As they sat there, waiting to talk with the other doctor, The Caramels whispered into each other's ears on their thrill and excitement on being expecting parents. They are the first success.

Calming Seabreeze is just coming back from the examination room after checking to see if she had become pregnant. She's the twenty fifth mare volunteer that they checked and she's the second success that the project's scientists has had so far and will be having a filly in the upcoming months. She also just had a talk with the doctors about the future between her, her husband Salty Seabreeze, and her expecting foal to The Alicorn Project and its staff.

She has been told that both of them must stay at the facility through the duration of the pregnancy. She may write to her friends and family, but she must not mention her foal or the project. After the birth, she may then leave and visit whoever she wishes, but must leave her foal behind and never say anything about the project. This was, of course, made aware to her before she volunteered.

They will be staying in modest quarters while the facility is being completed. The quarters have everything a pony needs. A bedroom, a living room with a mildly comfortable couch, and a bunch of CDs with a radio. The CDs are mostly DJ-Pon3 and Octavia albums. The facility has a cafeteria so at least she or husband wouldn't have to cook. They were told that they can decorate it however they wish.

She knows that she's incredibly lucky. Even if she could have foals on her own, there would be no way she or her husband could care for one without aid. Her husband used to be in the navy, but had a crippling injury to his left hind leg that gives him trouble trotting around. With him unable to do physical labor, how could they support a foal? With their finances, they could never adopt.

Now that's not the case. They can now have their own foal and support the so to be filly with this project. Having a foal of their own, have all the support they will need, and support a great cause, how could they ever say no?

Calming stood next to her husband, taking a look around at the sightly bare living room.

"She's bit of a fixer upper, isn't she?" she said to her husband.

"Nu'ting that picture of me an' the lads wouldn't fix." Salty said in reference to a group photo of his old crew mates. "Ya, aye think it'll look good right 'bout..." he slowly hobbled to a bare part of the concrete wall by the radio, "here." he pointed to the wall.

"Well, I suppose that's a start. We can think about later though. The doctor said we should get to know the other lucky couple, The Caramels, I believe."

"Aye, but why not relax a little? We're 'bout to start a family after all."

"Sure, why not?"

Breezy Gale is in the examination room checking with her coltfriend, Wild Storm, to see if she got lucky with this experiment. Having a foal will make their choices up to this point worthwhile. Wild had a career as a Wonderbolt ahead of him, but give it up to start a family with Breezy. Breezy enjoyed the idea of spending her life with him and a foal or two, but Faust had other plans for them. The pain after that dreadful fertility clinic visit is something she hopes to put behind her with the project.

She is the thirty eightieth mare that volunteered for the project. She has been told not to hold her breath, but not loose hope.

The doctor is looking over the scanning crystal's screen and then she grows a look of concern on her face. She quickly calls in another doctor.

"What's the matter? Is there something wrong?" Breezy asks the doctor.

"I'm not sure. There doesn't seem to be a problem, but there's something unusual."

"What is it?!"

"If something is going on, I suggest you tell us." Wild added.

"I'll have the other doctor explain it as soon as we figure what is going on."

It didn't take long for the other doctor to come rushing in.

"Is there an issue?" he asked.

"I'm just trying to figure out this... anomaly."

The second doctor trotted over a looked over the screen.

"I'm not seeing anything out of the norm."

"No, look here and here."

The second doctor paused then exclaimed, "Oh! Now I see."

"I know, but I'm not sure how it happened."

"No scientist really knows why it happens, but it's a pleasant surprise none the less."

"Can somepony explain what's going on!" Wild burst out.

"Should I or do you want to?"

"Well since you're here."

"Very well." The second doctor composed himself. "This doctor was just confused by the fact that there are two implanted blastocysts instead of one. I can only say that though some miracle of Larson's, the fertilized egg cell spilt in two. So may I be the first to congratulate you two on your identical twin colts."

Open and Grassy Meadows are sisters. They are coming back from the examination room and both of them ended up lucky. They are the forty seventh and forty eighth volunteers. They both had successfully become pregnant with fillies and are heading to their quarters at the facility with their husbands, Empty and Field Meadows, whom are brothers. They are talking about every witch way to decorate their quarters.

Open wants to make her new home feel like nature. She has always loved nature. Both her and her husband, Empty Meadows, were park rangers prior to volunteering for The Alicorn Project. She wants to have potted plants, soothing music, and her and her husband's ranger uniforms displayed.

Her sister on the other hoof, wants an indoor garden. She was always growing all sorts of plants at her home. Her husband, Field Meadows, worked as a farm worker. They met each other at a market while Grassy was picking up seeds and fertiliser and Field was selling from a vender. After about a year of going out, they introduced their siblings to each other.

Surprisingly, both mares are infertile and it's not for genetic reasons. It's really just some cruel twist of fate. However, the fact the experiment is a success for both of them is a real sign that things are turning out for the better. Now the two couples plan their foal's new futures and the new friendships with the other three successful couples and their foals. Life can be good like that.

"Our prayers have been answered, thank you Larson."

"Yes, I can say we have a success that is too good to be true. Five successful pregnancies, which is of course, five more than we expected. One of the pregnancies has also yielded us identical twins. Work on making the facility capable of holding the future alicorns is underway. So yes our faithful investors, the project is proceeding as planned. Now we must address a major issue. We all have different opinions on what shall be done when the alicorns mature. Whether we should replace the princesses by usurping them or going off to lands unknown and follow them there, or simply add more alicorns into the world and force the princesses to recognize them as royalty as well or have them replace the dukes and counts of the land and have the feudal system with the alicorns instead. This is an issue I see that will take much time, but the alicorns we have right now aren't going to ready to do anything for a long while. So, let us begin with the first session we'll have on the topic."

The Parents

The five couples met up and began to chat amongst themselves. The mares in one group and the stallions in another

"So Creamy, how did you meet your stallion?"

"Well, me and Brown had families that worked together. We found ourselves working in the same candy shop. After a while, we started to date."

"So when did the question pop?"

"You mean the marriage proposal? One day I came in the shop early because he asked if I could and I found that he made me a giant heart made of red and pink gumdrops with some green ones to make it look like an arrow going through it. He had a few purple and blue ones in the middle that spelled out 'will you marry me?' and how could I say no?"

"It's different, I'll give you that."

"What about you Calming?"

"Salty came into the bar that I tended quite often. We would talk a bit and, after he had a few drinks, he'd flirt with me. We never went beyond that until he had his accident. He didn't have much family and most of his friends were his crewmates that were away for long periods of time. He needed somepony that could care for him, and so I did. After caring for him like a nurse, we just sorta came together."

"Well, me and Wild haven't married yet. I know he was going to because he left The Wonderbolt Academy so he could spend more time with me and be an attentive father for when we decide to have a foal. Fate tried to take that from us, but instead, we're having two. Knowing him, he'll probably tie the knot after the pregnancy."

"So how did you two meet?"

"He was my high school sweetheart. We went to prom together."

"My sis dated my stallion's brother. Her coltfriend asked for our help on his farm, as we were gardeners, and I worked with Empty and we drew closer."

"Open also caught the bouquet at my wedding."

"And I married Empty the next year."

"Now both of you are pregnant. Strange coincidences."

"Indeed."

The stallions are playing a card game and chatting amongst themselves.

"So what is that you do, or rather, have done, Brown?"

"My family are a bunch of shop owners. They have a partnership with my wife's family and they run a number of shops around Equestria. I found myself working in a candy shop with the mare of my dreams. I liked it. I was always good with foals and now I'm an expecting father. I can't wait until my son is brought into this world."

"And for such a good cause too."

"Yes, me and my wife believe that every time something happens in Equestria, it's a gamble. We need a little bit more insurance for such things."

"Aye! Now that's some'ing I can agree with!"

"Hey, do you mind sharing how you got that injury, Salty?

"Sure, but be warned, 'tis is a horrifying, cringe worthy tale."

"Get on with it then."

"Well, I was in the navy and me an' my crew was out on exercises at sea an' we were hit by an unexpected storm. Our ship was knocked around like a toy in a bathtub. A heavy crate sid off the upper deck an' landed on my leg."

"You were hit by a storm? Why weren't you informed by weather ponies?"

"The sea works much differently from land. The weather is like The Everfree Forest except less... everfree. Weather there works on it's own."

"Okay then. You say that a crate landed on your leg? As painful as that sounds, doctors can use magic to heal even multiple fractions. So why is your injury premendent?"

"Keep in mind that darn crate was on my leg the whole time and the ship was being tossed 'round by the wind and waves."

"So that means..."

"I was tossed 'round like a rag doll. The only thing I could hear was the crashing of the waves, the howling wind, the creeks of the ship, and the cracking of my bones. As I was flailed 'round, I got to see my leg bend an' twist like it was made of rubber. In the short looks I got, I could see bits of bone sti-"

"Stop! To whatever god will listen, don't let him go any further!"

"That's all it takes for you to cry out for mercy? Wouldn't last a day in the navy, that I know. Anyways, It's true that multiple factors is no problem for unicorn doctors, but the bones in my leg were like powder. What you see of my leg is what the doctor were able to fix. Was lucky that my leg didn't rip itself off, that I was. While I has at home, healing, Calming came to me like an angel an' took care of me when nopony could."

"So are you about done?"

"Oh! So the wild one wants to talk about himself?"

"All you talked about was your poor attempt at gross out and mentioned your wife."

"Well I made him beg for a god to grant him mercy, but since you have some'ing much more important to say, why don't you tell us 'bout your Wonderbolt career."

"I left the academy to prepare a new life with the love of my life."

"Aw. Now ain't that just sweet. Since you volunteered to the project, I can asume that didn't turn out too well."

"And now I'm having twins. At least I didn't just fall in love when needed to be babied."

"Hey hey hey. Easy."

"Don't worry 'bout it. I'm not nearly sober enough to care 'bout what he has to say."

"It's not like you can do anything about it."

"And what would you boast 'bout to your sons? That their athletic dad beat up a drunken cripple?"

"Well! Before we get anymore passionate about our macho contest, let me and my brother just say that we are playing a game right now."

"Yes brother, let me just say, Royal Flush!" Empty shouted and slammed his cards down, followed by the groans by the other stallions.

The pregnancies progressed normally.

After a couple months, the fetuses developed to the point when they are recognisable as ponies. At this point, a few of the mares began feel strange. Creamy feels very hot, Calming feels calm and relaxed, and Breezy feels energetic. The doctors and scientists are concerned about this, especially Breezy for the twins. The twins are the main focus of the project because it's become well known that a pair of twins that has a unicorn in the pair tends to affect the DNA of the other twin. A case of this are the Cake twins. Pound Cake is a pegasus, but Pumpkin Cake is a unicorn. By what was found, the Cakes are earth ponies and because the earth pony trait was dominant to the others. So in order to have any other kind of pony, both Cakes must have a recessive trait and pass on the recessive trait to both of the twins. The unicorn trait is dominant, but Pound is a pegasus, which is recessive the unicorn trait and the earth pony trait. It's theorised that Pumpkin's unicorn magic radiated (think nuclear radiation, but less dangerous) when they were in the womb and mutated some of the DNA in Pound, making him a pegasus.

Breezy's twins are supposed to be alicorns and the magic that they could radiate concerns the project. The twins are put under close observation.

As time went on, the project's staff breathed a sigh of relief as both horns and wings began to form on the fetuses. The mares feelings however, only grew stronger. Creamy is breaking out in sweat, Calming is relaxed to the point of fatigue, and Breezy can't sleep. The problem does seem magical. The project simply hoped that the issue will go away after the birth.

"For eleven months we have discussed where the project will go with our alicorns when they mature and the only thing we can agree on is we can't just remove the princesses, at least not easily. Between Discord and the harmony friends won't just let us come and take Equestria. Most of us can agree that many dukes and counts are corrupt and unlikeable. Our best hope is the princesses will install our alicorns in the place of normal leaders. However, some of you disagree. The births are expecting to happen in a couple of weeks and it'll still take a number of years before we can do anything. Let's see what our alicorns can do and we'll hopefully come to an agreement."