It all started when Alyssa had children. MIYU, the android created to watch over Alyssa until the war was either over or the girl died, was given a new directive by her master.
Protect her children until the line died out or Miyu was defeated in battle. But, she wasn't too allow them to cause too much trouble. Miyu took that new directive to heart and became the silent guardian of her young miss.
Over a thousand years later, and her directive was still the same. Protect Alyssa's children. What Alyssa had been unaware of was that her blood was special. In it was a special gene that would make blond hair almost genetic. In Miyu's eyes, those children shined like gold.
Her travels lead her to the Hidden Village of Konohagakure. She was about to go to the bookstore when she saw a young child being beaten within an inch of their life. Miyu would have ignored it, but the child had golden hair...just like Alyssa.
The fool was dead before he realized what happened, and Miyu took the child into a forest. By the time anyone realized what had happened, no one had a good description of her.
There was also the fact that since Miyu had no chakra or any actual scent meant that the ANBU couldn't track her.
(A useful fact she learned when the shinobi profession first came on the rise. She had even meet the legendary Rikudo Sannin in his prime and knew him personally. He found it fascinating that she knew what the red star was that most people had forgotten about.)
Miyu did her best to treat the kid's injuries, but she quickly noted it wasn't needed as they started to close with a hissing sound. Her scanners told her that the child (female) had a bijuu sealed inside of her, and that the demon in question was in fact the Kyuubi. She gently placed a cloth on the girl's head to cool her down.
Even with advanced healing, using Kyuubi chakra had a habit of overheating the user.
"Who...who are you?" asked the girl.
"My name is Miyu. I was asked long ago to protect you by your many times great-grandmother."
"You...you know my family?"
"I do. And Alyssa would never allow her grandchild to come to harm. Now, stay here while I go retrieve some food," said Miyu.
"Okay!" said the girl. She hid under some roots and was perfectly invisible...to everyone except Miyu. That golden light would lead her to the child no matter how far she was.
Miyu returned with more information than before.
The girl's name was Naruko Uzumaki, named after her mother's clan. Considering how famous the Namikaze name was and the probability of an assassin because of it, the fact she was named Uzumaki was acceptable.
The next thing she learned was that her new charge was deliberately being neglected, held back, even beaten by the village. Very few dared to openly be kind to her.
Of those few were the Hokage, the owner of a small stand and his young daughter, and a single teacher out of thirty at the Academy.
Those she really worried about were the council, the select group known as ROOT, and those known only as Akatsuki.
She had a few run-ins with them, but they never ended well...not for that old one and his ever changing partners at any rate. (Kakuzu)
She found the girl still where she left her, and she showed enough common sense not to immediately approach.
"It's alright little one. There's no one around for exactly five kilometers," said Miyu.
She had long since calibrated her sensors for chakra, rather than electricity. So much more reliable than tracking through whether or not someone had a cell phone or something on them.
The girl cautiously came out, scanning the area like a fox would. Finally she bounded up to Miyu with a smile on her face. Once she had eaten, Miyu scanned the area around the girl's home for anything suspicious.
When she found nothing, she let the girl in. Thanks in part to the fact she could change her hair and face on a dime and had no scent, no one would know who she was in the morning when she left.
"Now remember what I told you," said Miyu.
Naruko nodded eagerly. Miyu was so much nicer than everyone else.
She went to the Academy pretending everything was fine and kept Miyu a secret.
Part of Miyu's request was that Naruko not speak of her, and if she had to, then to make up a fake name and face.
Miyu had said she would take Naruko with her the first chance she had, away from all the angry glares and beatings. That was all she needed to hear...well that and it would be a prank that kept on going for years if they played it right.
Once she was gone, Miyu systematically went to cleaning the apartment. She sealed all that would be taken and made a note to trash the rest. If they were going to make a clean break from this village, then they needed an air-tight alibi for why they weren't there.
And the easiest way to throw off pursuers was to fake the girl's death.
Three months later...
Miyu heard the screams of the so called 'great Uchiha clan' on her way to Naruko's apartment. She knew her time had come.
She gently shook Naruko awake.
"Naruko, it's time to go."
"Okay Miyu-nee," said Naruko sleepily. Miyu had drawn enough blood to fool the hounds and she planned to burn the apartment down.
By splashing blood here and there, and erasing all trace of their escape, it was unlikely they would even know that the girl was alive. Plus with the massacre, it would take days before anyone thought to check out the tale.
It wasn't the first time Miyu had to perform an extraction, though last time it had been in Water country. She was considered one of the strongest supporters of the Resistance in Kiri, because she helped those with bloodlines escape to those seeking to replace the current Mizukage.
And they would most likely be happy to help train Naruko for a few months while she set things up. It would be too dangerous to travel with a young girl until she knew the basics. At the very least, she didn't want word of a young blond with blue eyes seen anywhere near Fire country until she was old enough to defend herself.
Mei was in shock when the infamous MIYU appeared with a young dark haired girl beside her.
"I don't believe it. I thought you didn't get involved directly Miyu?" said Mei.
"You remember my current primary directive. Correct?"
"Ah...so she is?" said Mei.
They had once approached Miyu with offers to formally join their Resistance. However the 'girl' had said that she had promised her young Miss that she would protect her children until her deathbed.
Which meant this child was one of those children.
"Her name is Naruko, and I was hoping you and the others would teach her how to be a real kunoichi since I still have to get things set up."
"Raising her on the road then?" said Mei.
"Faked her death to insure no one tries to 'rescue' her."
Mei bent down to eye level with the recently dyed Naruko. Her hair was pitch black at the moment. Her blue eyes were now green, and she wasn't wearing any boy's clothes.
It had been ridiculously easy to leave the village without using a henge. So many people forgot the old ways of hiding, before the use of chakra.
Mei nodded. It would be the least they could do for Miyu, because if she hadn't helped, at least ten clans would have died out entirely.
One year later...
Miyu returned. She had come back off and on to check on Naruko's progress, but it had taken this long for the aftermath of the Uchiha Massacre and the 'death' of Naruto Uzumaki to settle down in Konoha.
Thanks in part because no one knew the girl was not only alive, but thriving and no one knew who Miyu was, it was finally safe to take Naruko on the road. There was also the fact that Naruko's hair had grown out from that rat's nest she had been forced to wear it as for as long as she could remember. Now it reached her neck.
Because everyone believed 'Naruto' to be the Kyuubi reincarnated, no one would be looking for a girl. Miyu had checked, and it seemed that Sarutobi was so used to Naruto that he had forgotten that the poor child was really a girl.
Little Naruko's outfit had changed as well. Since she was the 'ward' of Miyu the Golden Sword (her nickname...she even had a BINGO book listing!) she was given special treatment.
Naruko was at least Genin level now, so she could handle a few bandits. Her chakra control had shot up since introduce to water walking, and she recently learned her element.
She was a rare Wind-type.
Naruko ran up to Miyu and hugged her, showing off her new dress. She was beyond thrilled that she no longer needed to hide that she was a girl anymore.
Mei had been particularly pissed off about that. She insisted on getting the girl a new dress to wear when she heard about what the Hokage had convinced the girl to do.
"How has she progressed in her studies?" asked Miyu, placing a comforting hand on Naruko's head.
"Very well, considering she's not even ten yet. She has a natural knack for jutsu, though anything below E rank will be impossible. Her reserves are ridiculous," said Mei, eyes narrowing. She had an idea why too, as spy reports claimed the current container of the ninth bijuu had died very recently.
She wasn't going to try anything, because she also knew Miyu would kill her before she came close.
"So will you be returning?"
"We will stop by whenever we are in the Land of Water to deliver supplies."
Naruko beamed at Miyu. She had made quite a few friends here and she would be thrilled to see them again.
Jiraiya was on his third bottle when the blue-haired beauty with red eyes walked in with a little girl with red hair.
She looked so much like Kushina that it nearly broke his heart to see that girl.
"Miyu-nee, can we get some ramen?" asked the little girl.
"You can't keep eating ramen Naru-chan," said Miyu,
"But I did the exercise you showed me perfectly!" said the little girl.
"Alright, but only three bowls. After that you have to eat something like gyudon or onigiri with vegetables," said Miyu.
Jiraiya wouldn't have paid any mind to the girl, except there was something about her that bothered him. He kept observing her and little things started to remind him of Minato or Kushina.
Finally, the clincher. A small smudge on the little girl's check that revealed a line, almost like a whisker mark.
Naruko had whiskers marks, three of them. He didn't notice that the older girl was glaring at him.
Jiraiya stopped them just outside town.
"Who are you two?" he demanded.
"Miyu-nee, he's creepy," said the little girl.
"Yes, but he's also the best seal master in that village as well as a competent shinobi when he isn't being an annoying pervert."
"He knows seals?" the girl perked up.
"Yes. He taught your father many years ago," said Miyu.
"I'll ask again, who are you? Don't make me ask a third time," growled Jiraiya.
"My name is Multiple Intelligence Yggdrasil Unit, or Miyu. I have been tasked by my master many years ago to protect her descendants. I have rescued her from an abusive situation and I will take it poorly if you attempt to return her to that village," said Miyu coldly.
"And the girl?"
"I can only assume you know who she is, otherwise you would not have accosted us outside the town."
"She's alive... Thank kami-sama..." said Jiraiya in relief.
When he heard the news that 'Naruto' had been killed in an explosion the same night as that massacre, he had feared the worst for his goddaughter. He did worry, however, that his old teacher had forgotten that Naruto was in fact a girl.
"If you wish to discuss this, I suggest you meet us in the inn. But make no mistake, she isn't going back until she is at least Chunin or Jounin level," said Miyu.
"So what really happened?" asked Jiraiya. He had bought several bowls of ramen for the girl and she was lost in her meal.
"I located Naruko being beaten by a village and killed him. Once she was healed, I started preparations for her removal from the village when I realized that the villagers would not change anytime soon and my charge would be in mortal danger as long as she was in the village. This isn't my first removal."
"Why did it take you so long to find her?" asked Jiraiya.
"I traveled the world many times, and the only way I can know if someone is of the same bloodline is something only I can see. One of the most visible characteristics is golden hair."
"Those of Alyssa's blood tend to have impacts on history. Minato was just one of the more memorable ones," said Miyu flatly.
"How do I contact you?" asked Jiraiya.
"If you leave a note in the bounty stations for the Golden Sword, I will contact you. For now, Naruko will travel with me," said Miyu.
"Is it alright if I teach the kid a little sealing?"
"That is the reason we came near the town, even though your chakra signature was in it," responded Miyu.
Jiraiya grinned. Finally, things weren't looking so miserable. Perhaps he could send the girl Tsunade's way as well...kami knows she needed a reason to believe in life again.
Then a thought occurred to him.
"So which one was of Alyssa's bloodline? Minato or Kushina?"
"Minato. Kushina also had the blood of another like Alyssa, but her bloodline was different than Alyssa."
"Kushina had a bloodline too?"
"She was the descendant of Tokiha Mai, a woman who defeated Alyssa many years ago...but she also freed her."
As Miyu describes some of the powers the two had Jiraiya made a note of which books to give Naruko. By the time they parted, Naruko had a basic idea of how seals worked, and several books on how to make her own. Not that Miyu would allow her to try them unless Jiraiya was around to insure nothing went wrong.