Disclaimer: Naruto + Fairy Tail - I own neither
Rewrite of "Naruto the Apprentice of the Fairy Queen"
Story Start!

"Changes to Genetic Code are stable, very stable... This chakra is a magnificent bonding agent." A deep male voice stated. The owner of the voice was a tall person, standing at about 200 cm tall exactly. He was an older man, with a bald head and several wrinkles on his body, mostly around his face. Despite his age, he seemed well muscled with only a slight amount of muscular decrease over the years. He wore a white lap coat, which had dried blood stains on the sleeves and around the corners of it. The man had dark green eyes, and he was staring down at the body that he had found not too long ago.

The damages to the body had been extensive, very extensive.

He had been witness to the battle that had caused these injuries, and the battle that had caused these had been nothing short of fantastic. The power this young body had was nothing short of stellar.

1 freshly healed hole in the chest, with another fresh hole in the chest to start off. A broken neck, several dozen broken bones scattered all over the body. A missing arm and leg, both of which had happened during the last attack. A large amount of chest missing, as in the muscle and flesh on the chest and not the bones of the chest. The last attack between these... Rasengan and Chidori had been amazing for him to see. During the last second though, this young boy had managed to hold himself back and created a weaker Rasengan made to injure... while the other young boy had created a Chidori made for murder.

The other young boy had been knocked out cold with a missing arm and large friction burns on his chest, but the man had no interest in that boy. He had too much hate in him, a desire for revenge and blood. He was not somebody that he wanted to gift anything to.

This young boy though, was the opposite, sunny and filled with both love and forgiveness.

He had to have him, so he had kidnapped the boy and brought him back to his Genetics lab.

Shinobi, a trained being that was trained in the use of chakra. Chakra was an energy used by battle produced on the inside of the human body. It did many things, but one of the least known things it was used for was Genetic Code modifications. When a chakra user was injected and given the DNA of other beings, and assuming they didn't die, their bodies started to modify their bodies to assume the shape of the DNA that they gained. Allowing them to access new abilities and change themselves.

Naruto Uzumaki, the boy's name.

He was currently wrapped up in bandages from head to toe, with only small amounts of his body showing. He had the bandages on his right arm and leg done up more seriously. He had recently transplated a genetically modified arm and leg to the boy. It would take awhile for those to become fully attached to him.

"Uuuuuuuuh." Naruto's pained sound came out of his throat, the voice of a young... person about 13 years old. The man didn't know to much about this all, he just did genetic research using his ancestors genetic supply.

5000 Years of Collecting and Preserving the most powerful Genetics the world had to offer. 5000 years of his family using hidden abilities to preserve bodies, only keeping the best of bodies for experimentation. He had been using the best of his collection to fix Naruto up, and change his DNA as much as he could... or rather, the changes would happen on their own given enough time.

He had been carefully recording the progress that Naruto's DNA had been making over the last 3 weeks, changes were only slight at the moment.

It would take at least a few months were the most noticable... changes were made evident. The boy had survived the beginning changes though, so that was good enough. He survived the first week, meaning that his body would survive the changes he went through. he had a very durable body, with an extremely strong life force.

"Shhhhhh." The man said as he injected Naruto with some pain killers, strong enough to affect him and keep him out of a sane mind. He was not a fighter, if Naruto woke up it was possible that he could be overpowered by the boy and all his hard work would be destroyed. He had spent nearly a month keeping him sedated, just so that he wouldn't move around and disrupt anything.

He looked at the machine that was hooked up to Naruto's chest, just above his heart.

XY - XYXXXX
br - brrrww
Ss - Ssssss
bp - bpBbbb
T90/E10 - T10/E90

The screen showed the progress of the genetic changes, and what he should be expecting. The normal Male Genetic Code was XY, with the X being female and Y being male. A person inherited one side of their genetics from both parents. A father would pass down a X or Y, which decided the gender of the child. The mother could only give X, because the female genetic code was XX. One side of DNA came from each parent, but that wasn't what was happening here.

For the transplant of genetics, he had given Naruto the full genetic code of two seperate females... whose bodies had been among the first of the collection. Instead of only adding a single X per 'donor', each donor provided the full XX genetic code.

This showed that young Naruto would soon begin to experience some very noticable changes in his body that were female in nature... his new Genetic Code was Female/Male/Female/Female/Female/Female after all. His body registered only 1/6th of the DNA as male at this point. That alone was causing changes in the brain to happen, increasing production of female sex homrones and decreasing male sex hormones. That part had already become fully stable, so once puberty started the changes would start to rapidly happen.

Naruto's hair was going to turn red would be another change, one that would start happening when his hair started to grow out. The br code was his original, and those traits were both weaker genes. Naruto had the gene for both Blonde hair and Red hair in his body, with blond being more dominant. Red hair was a weaker gene that needed both parents to pass down red hair for it to become the hair color... the same with blond actually, but blond was a little bit more dominant.

Now though, with the changes made the code was brrrww or Blond, Red, Red, Red, White, White. He had three Red Haired Genes, two White Haired Genes, and a single Blond Hair gene.

Red was the current most powerful gene in the body. This also tied into his hair turning straight, he had a single gene for spiky hair, and five genes that told his hair to become straight.

Thankfully thanks to chakra, his body would be able stay somewhat normal as it made the changes. It was truly like a glue, keeping his genetics from going out of control and keeping a human form. Naruto also had a strong resistance to mutations himself, which was a great thing for him.

"Hmmmm, I like this shade of blue." The man spoke as he opened one of Naruto's eyes and saw the shade of blue that he had them at.

He was glad Naruto was going to keep them, they were pretty.

Blue-Purple, that was the precious code Naruto had for his eye color. He had gotten nice blue eyes, and he was going to keep them. Brown was a dominant color, but thankfully only a single gene on the entire addition he added had brown. One of the females had brown eyes, but she did have the gene for blue eyes in her. The other female had two genes for blue eyes, meaning that Naruto had four genes for blue eyes, one for brown, and one for purple. He would get to keep those blue eyes, very expressive blue eyes.

"Raaaaaamen." Naruto spoke in his sleep, before he looked like he wanted to turn. "Caaaaaaake." Naruto said right after, like he was in an internal debate with himself. Personality, despite what people though, was very much attributed to genetics and how they affected the brain. Food preference was the same, Naruto seemed to have an unhealthy addiction to ramen... while many females had a food preference for sweet things. One of the females must have had some sort of addiction to cake, while the other simply enjoyed it if it caused an internal conflict.

Interesting.

"You are quite lucky, sweets are better for female hormones. They help in production and growth. I wonder where the ramen food preference comes from though?" The man stated to himself. He had undergone so many genetic transplants on himself, that he had LONG since forgotten his own name. He transplanted many things into himself, and had barely been able to remain stable. He transplanted parts of the most intelligent people to ever exist into himself, in the hopes of gaining the ability to understand more of the human gene.

He placed his hand on Naruto's chest, where he had to do a major flesh transplant using cloned flesh. He had cloned the flesh from one of the donors, and used that cloned flesh while matching it to Naruto. Of course, it was a few shades lighter than his peach colored skin... but with enough sunlight that would go back to being peach color... or Naruto would gain a fair pale skin color. He was curious about which one would win out, though he suspected the lighter one.

Naruto had a single gene for peach skin, and currently five genes for fair skin.

He placed a hand-held scanner above Naruto, this way he could see inside of his body. It was an organ scanner, created a long time ago and only recently fixed up. It had a screen on it that would show the insides. It was based on ultra-sound technology, only somebody who could read an ultrasound would be able to understand the results.

He had done some... open body surgery on Naruto, removing any damaged organs and replacing them with cloned bodies of the genetic donor's organs... cloned up to the point that they would match Naruto in age.

He didn't want to damage the preserved bodies in his collections, so he cloned anything he needed and used that... before he threw away the clone body.

"No issues with tissues, bones are just fine and restructuring well enough for now. Possibly a month of physical therapy, or less if the healing factor holds up true." The man noted. He had only replaced a few things. He replaced the right lung for one, and he had replaced the stomach completely... The boy's stomach, while in perfect health, did not digest very well. It didn't completely do what it was suppose to do.

The lack of nutrient digestion didn't give enough nutrients to the body to grow, so a bad digestion system could be blamed on genetics.

Or he was simply a late bloomer who didn't grow much until after puberty.

"Ramen cake." Naruto said, his mind deciding that he wanted both at the same time. He was pretty much asleep, but at the same time not asleep. He was out of it that was for sure, but over the last week Naruto had started to get used to this level of drug dosage. He wanted to up the dosage, but that might affect how stable Naruto was. He was in the process of making sure that there a 100% stability rate.

Anythingn less, and there was the chance that Naruto would undergo extreme amounts of pain thanks to a quickened transformation.

A high stability meant a slow transformation, but a painless one.

He didn't notice a shadow move behind him, not even a single time. Several shadows actually, he was not a ninja and hadn't developed a sixth sense for when he was surrounded. He didn't see the eyes that were following his movements, and narrowing in anger behind him. Multi-colored eyes, one eye a black color, and the other eye red with three black tomoe around the pupil.

The tomoe were spinning, and the eyes moved closer to the man as the shadow became lit up and turned into the form of a man.

A pissed off Kakashi Hatake, who had been searching for Naruto for quite a long time since his disappearance. He was a tall, lanky man standing at around 5'10", with silvery gray hair that stuck up and pointed to the left side. He had his leaf headband on his forehead, and wore a green flask jacket with several scroll pockets on the breast pocket. He had a blue long sleeved shirt and armored gloves, as well as blue pants.

The other shadows were men and women dressed in various uniforms, all the same but modified for gender. Their features were hidden by cloaks, only white masks showed who they were too Kakashi.

Lightning sparked in Kakashi's hand, before he shot towards the man that had kidnapped Naruto. With a single stoke, Kakashi pierced right through the man's chest, his hand bursting through one side and coming out the other. The man gurgled as his heart and lung were pierced, and Kakashi pulled his hand out of the man's chest and watched as he fell to the ground.

"Raikiri scum, don't kidnap a Leaf Shinobi, and you will burn in hell for kidnapping my student. Anbu, collect all of these papers and clipboards. This sick bastard was doing experiments, don't leave a single speck of information in this place, and burn it to the ground." Kakashi told them all, and the Anbu Squad... a squad of 14 men and women strong... listened to the pissed Kakashi without hesitation. They all started to go around and gather materials that they found.

This place was going to be burned to the ground the second that they were able to collect what they found.

The Anbu were a silent attack force, soldiers who were follow orders without making a single unneeded sound. They did their jobs, while Kakashi went over to Naruto and saw the IV attached to him. He gently pulled it out and fixed the bandages so that they stopped the bleeding. Kakashi picked Naruto up just as gently, since they had found an arm and leg at the Valley of the End he knew that the current arm and leg Naruto had were not his own... and while he hated to admit it, he didn't want to ruin whatever sick work the man had been doing.

Lady Tsunade was going to be pissed the hell off, but she would want every speck of information to look over.

Kakashi shifted Naruto onto one of his arms, so that he had a free arm, before he picked up a chart with letters and numbers that he didn't understand. Some sort of code?

"Kakashi-senpai, there are bodies... and a lot of them in the next room. Perfectly preserved, and some of them are... One of them is the Fourth Hokage and Lady Kushina." An Anbu said nervously, knowing that Kakashi's temper was shorter than it had ever been lately. Honestly, the last three weeks had been hell for anyone that had said something wrong to Kakashi. The man beat the shit out of any person that got on his bad side.

"The Third Raikage... the Second Tsuchikage... this guy has some very... He has been doing this for awhile." A different Anbu stated, and Kakashi took note of it. This person had been collecting bodies, but for what reason... not that it mattered with him dead. He was pissed off, sure... that explained a lot about how people's bodies had been going missing for a long time actually.

They had been collected, only the strongest seemed to get added to the body collection.

"Lady Tsunade will want to see this, gather bodies and seal them away. Gather everything you can, I will head back to the village." Kakashi spoke dead seriously as he started to walk towards the exit. His mission would be completed the second Naruto was home safe and sound. Despite what people seemed to think, a good number of people were worried about Naruto.

This was some kind of Genetic lab, and tests needed to be ran on Naruto as soon as possible to make sure that no... harmful changes were done, not that they could be stopped if they had been done.

There was no rewind button on genetics, no flipping a do-over switch. Any damage done, if it was damage, was permanent.

"Kakashi, wait... it seems that each body has a notebook containing their name, history, and skills." The same Anbu that first spoke, spoke again as he showed the Minato Namikaze notebook and the Kushina Uzumaki notebooks to him. Kakashi looked at them, before he furrowed his brow.

"Take them all, take everything." Kakashi said, before he turned to leave again. This time nobody stopped him from leaving.

It was time to go home.

Chapter End!
Kurama is not a Demon, so Demon Take-Over does NOT work on him. Also Erza's changes to fit size, not gender. Velveno used her armor, and it stayed female armor.
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