The Third Hokage sat at his desk. He sighed and took a puff of his pipe.
It was five years ago when he first revealed the existence of Uzumaki Naruto and Kuzumaki Haruto to the village of Konoha…
"This child is the Kyuubi's jinchuuriki."
The ninjas glared daggers at the blond baby wrapped in an orange blanket.
"His name is Uzumaki Naruto. He is the container of the Kyuubi to protect us all."
The ninjas murmured to each other.
"The Kyuubi's still alive?"
"It's not going to protect us! It's going to kill us!"
"Bullshit! The Fourth Hokage died because of the Kyuubi! Why are we even keeping it around?"
"What if the Kyuubi broke free and returned? What would we do then?"
"If we don't do something, it'll destroy us!"
"Enough!" the Third Hokage commanded.
Everyone was silenced instantly.
The Third Hokage handed Naruto over to a medic-nin. Then he cleared his throat. "The Kyuubi killed many of our loved ones, but not all is lost. One baby girl survived being born during its attack."
Another medic-nin brought out a black-haired baby girl wrapped in a purple blanket.
"Look at this child who survived against all odds. Isn't she a miracle?" The Third Hokage smiled down softly at the baby. "Kuzumaki Haruto…"
The ninjas' faces filled with pity. "Poor girl…"
The baby girl yawned and opened her eyes.
People gasped in horror and disgust.
Any sympathy they held for the orphan girl faded away instantly.
"Those red eyes! Just like the Kyuubi!"
"Look! She even has the same whiskers as the other one!"
"Born on the same night of the attack looking almost identical? It can't be a coincidence! The Kyuubi's manifested itself in both of them!"
The ninjas' hands itched to grab their kunai knives, barely restraining themselves.
Their killing intent made the baby Haru squirm and burst out crying. Her cries awakened the slumbering Naruto, who started crying as well.
"How deceitful for the Kyuubi to take on the forms of two children to prey on our compassion! Well, that's not going to work!"
"Lord Hokage! How could we allow these beasts to stay in our village?"
The Third Hokage gestured for the medic-nins to quickly take Naruto and Haru away.
"Silence!" The Third Hokage's booming voice shifted everyone's focus on him. "All of you! Listen closely and listen well!"
"You are not to disclose the secret about the jinchuuriki's identity to anyone. Not foreign villages, not friends from outside Konoha, not even to your own children. Any who disobeys this order shall be punished with the severest penalty of our law."
The ninjas stood to attention. "Yes, Lord Hokage!"
"And you are not to harm those two children." The Third Hokage directed a hardened gaze at everyone. "Understood?"
The ninjas stiffened and shifted around uncomfortably. "...Yes, Lord Hokage."
The Third Hokage swept a hand over the crowd. "Good. You are all dismissed."
Ever since the villagers learned that the Kyuubi was still in their midst and treated Naruto and Haru cruelly.
The Kyuubi had instilled a deep, visceral terror within Konoha.
Konoha had never faced such destruction before.
Even so, when the Third Hokage revealed the existence of Naruto and Haru, he never expected the villagers' reactions to be so...violent.
No matter how much the Third Hokage and his subordinates tried to convince the villagers, they could never let go of unleashing their hatred on the poor children.
The Third Hokage rubbed his forehead, letting out another troubled sigh.
Taking on the mantle of Hokage again had a rough and difficult beginning.
Konoha was in shambles from the Kyuubi's attack and the Fourth Hokage's death.
The Third Hokage's wife, Sarutobi Biwako was killed in the battle. Her body was found under the debris of the collapsed building she and Kushina were in. - (She never got to meet her grandson.)
Since no ninjas from the Uchiha clan showed up for the battle with the Kyuubi, tensions with the Uchiha clan worsened.
Many children were newly orphaned and Konoha had to look into the care of its young more than ever.
Konohamaru…Naruto…the future generations of children who would carry on the hope of the Will of Fire.
And Danzo's Root division…a necessary function of Konoha's peace, no matter how much Hiruzen and Danzo disagreed with each other.
The Third Hokage's brown hair was now grey. As the years passed, his hands seemed to shake little by little while he did the paperwork in his office. He was growing older.
But Minato entrusted the Third Hokage with the safety of Konoha and his son. There was no one else ready as a worthy successor to the Hokage position. So the responsibility fell upon Hiruzen's shoulders (again, right after the death of another Hokage…First, it was the Second Hokage…now the Fourth…).
No one was able to find Minato's body after the attack. The body of his wife, Uzumaki Kushina, was nowhere to be found either. And so both the Fourth Hokage and one of the last living Uzumaki had vanished, denying anyone access to their bodies.
Later that night, the medic-nins informed the Third Hokage of another baby born mere minutes after Naruto. A civilian girl named Kuzumaki Haruto (or "Haru" as the girl had told him to call her).
The Kyuubi's chakra caused many babies to be killed in the womb or stillborn. So for Haru to have survived while not being a part of any ninja clan made her case a very curious and strange one…
The medic-nins ran medical and chakra tests on her to check if she had any traces of the Kyuubi's chakra inside of her. At the time of her infancy, Haru had none. They said that it was possible that the Kyuubi's chakra lay dormant inside of her, at least until her chakra coils fully developed. But, recently, the medic-nins confirmed in a medical checkup report that Haru didn't really have any of the Kyuubi's chakra at all. It was fortunate the girl didn't have to suffer through that burden.
That night of October 10, one baby was sacrificed to be a vessel to the Kyuubi, and the other baby was lucky to have lived.
Minato wanted Naruto to be seen as a hero.
Naruto, the Hero who kept the Kyuubi at bay, imprisoned its soul within himself.
The Third Hokage wanted Haru to be seen as a beacon of hope, a miracle.
Haru, the Miracle Child who survived being born during the Kyuubi's attack, despite all odds.
But alas, that was not to be.
And so Naruto and Haru were left orphaned and unwanted.
Only a select few people knew that Naruto was Minato's son, that the Fourth Hokage even had a child. They alone knew that Kushina was pregnant in the first place.
Even though Minato had many close comrades, it was not possible for them to safely take his son into their care.
The Third Hokage couldn't adopt Naruto. The boy's links to the Hokage would be made too obvious and people would question why the Third Hokage showed favoritism to an orphaned jinchuuriki.
Kakashi had enemies. Jiraiya had enemies. Anyone familiar with them and Minato would be out to kill Naruto when they found out about his relations with them.
The Third Hokage had already dismissed Kakashi from the Anbu. But the teenage boy only ever delved deeper into his shinobi duties. Kakashi couldn't seem to bear to look at the baby Naruto, reminded too much of his failure to save his mentor and his wife.
Jiraiya had left Konoha to travel around the world. He must have had important work to do, work too dangerous to involve his godson in.
As for Uchiha Mikoto and her friendship with Kushina…having the Kyuubi's jinchuuriki under the care of the Uchiha clan would only worsen its already tenuous ties with Konoha. The other ninja clans wouldn't have accepted that.
With no candidate available to safely adopt Naruto, he was put into one of the village orphanages with secret supervision from the Anbu.
Naruto was given Kushina's family name, Uzumaki to keep his identity safe.
Long after the Uzumaki clan's destruction during the Warring States Period, it fell into obscurity. After their small home village, Uzushio was destroyed, the survivors of the Uzumaki clan scattered throughout the world. Only Konoha's Hokages knew of all this through the knowledge carefully shared by Uzumaki Mito and Uzumaki Kushina in their marriages.
The Anbu reported that Konoha's villagers thought that Naruto was some nameless orphan the Third Hokage decided to give the Uzumaki family name to.
When Uzumaki Mito married the First Hokage, Senju Hashirama, the Uzumaki clan's emblem was added to Konoha's flak jackets as a gesture of goodwill.
So to see Naruto wearing the Uzumaki clan emblem on his clothing was not strange to Konoha's villagers.
No other ninja clan was willing to offer their name to the Kyuubi's jinchuuriki, after all.
As for Kuzumaki Haru, no family was willing to accept her either. She was promptly placed in the care of one of the village orphanages, a different one from Naruto.
The poor children…
During his spare time, the Third Hokage made sure to go out of his way to meet the children of Konoha, the budding leaf sprouts.
The young boy Naruto trusted the Third Hokage instantly at the first sign of kindness. He considered him a grandfather figure.
The young girl Haru regarded the Third Hokage with distrust. Such a guarded and cautious child…
The two children were like day and night.
The Third Hokage wondered how they might get along when they meet.
The Ninja Academy had just started a new year.
Naruto had enrolled in the Ninja Academy at the same time as Haru. But they were put into different classes. The villagers wouldn't stand for them being in the same vicinity.
The Third Hokage and his subordinates still had to keep the guise of Naruto being a normal orphan. So no private tutors for him. Let him learn alongside the other clanless children.
Naruto had been dragged kicking and screaming by his sensei into his classroom for the first day of classes. He hadn't even bothered to show up for the entrance ceremony, too busy preparing an elaborate prank for his grand entrance. So he had yet to meet Kuzumaki Haru face-to-face.
Ah. Perhaps the two children will meet when the time is right...
But what of their futures as ninjas?
Uzumaki Naruto, the son of the Fourth Hokage Namikaze Minato and Uzumaki Kushina was going to become a shinobi, no doubt.
As for the path Kuzumaki Haruto will take as a kunoichi…
The Third Hokage looked into his crystal ball, seeing Haru sullenly walk home with her hands in her pockets. He puffed his pipe.
…Only time will tell.
A/N: I found it so weird that Naruto's identity as the Kyuubi's jinchuuriki was meant to be kept a secret. Reading chapter 2 of the manga, it looks like all of Konoha knew about Naruto since the beginning rather than the retcon where Danzo leaked the secret later. I mean, the identities of the jinchuuriki in the other hidden villages were not kept secret. Everyone knew and feared Gaara and Killer Bee within their respective villages.
The Uzumaki clan was destroyed much earlier in the timeline in this AU. The Uzumaki clan being a mysterious long-lost obscure clan is cooler. It helps to explain how no one in canon said a word about Naruto being an Uzumaki or having him hunted down for his massive pool of chakra.
The Uzumaki and Senju clans are not related to each other.