Naruto belongs to Kishimoto. I'm just playing in his world for my own entertainment. No infringement is intended.
Prologue: Hidden Potential
The inky darkness of late night blanketed the streets of Konohagakure. With only a few lights shining around the streets, Sarutobi Hiruzen could almost pretend it was the Konoha of a year ago. Before the Kyuubi, before the devastation, when the village was still full of joy and laughter rather than suspicion and fear. Fom where he sat in his office, staring out the panoramic windows on an upper floor of the administration center, the view was peaceful, almost serene.
Behind him, his desk was covered with dozens of papers and scrolls arrayed in a messy scatter. Mission requests, reports, reconstruction measures - a thousand and one things demanded the Hokage's attention, and precious few of them were positive.
Konoha had suffered in the months since the death of the Yondaime. Meetings of the clan heads remained tense, full of finger pointing and accusations. The physical damage from the Kyuubi's rampage had been mostly restored, but Hiruzen feared the mental and emotional scars from the attack would never fade. Uchiha Fugaku had stormed out of the last meeting of the clan heads, furious at the blame Danzo and others had laid at his feet. Many in the village were already speaking of the baby jinchuuriki with disgust and loathing.
What really happened on that night, Minato? Who unleashed the Kyuubi on the village? Surely the Uchiha did not betray us. As always, Hiruzen had no answer to these questions. I'm too old for this, he mused as he puffed on his pipe, shoulders slumped and eyes off to the distance. Biwako, how I miss you.
A slight tap at the door brought him out of his musings. Early. Something must have happened. Taking a breath, he straightened and forced the tension and despair from his face. Hiruzen turned back toward the desk, re-lighting the doused lamps with a flicker of chakra. The pipe vanished into a hidden pocket, and he retrieved the red and white hat of the Hokage from where he had tossed it in disgust, placing it atop his brow. He took a deep breath and adopted the kind yet stern face he wore as the Sandaime.
A twitch of a foot triggered the hidden mechanism which unlocked the office door. "Enter," he called, disabling the traps with precise taps to the fuuinjutsu array under the desk.
A single masked shinobi slipped soundlessly through the cracked door and closed it behind her. ANBU Panther stepped up to his desk and wordlessly offered him a message scroll. The Sandaime took it and scanned its contents briefly. Most of it was routine reports, predictable - but the last sentence, hastily scrawled...
He laid the scroll down and turned his gaze toward the kunoichi. "Give me a full summary of the final item, Panther."
The cat-masked agent looked up. "Hokage-sama. A post-natal checkup on a baby in Konoha General Hospital uncovered indicators of a kekkei genkai in the child. The parents are civilians. The family was not on the watch lists. This knowledge has been confined to two medics directly involved in the case and myself."
The words were clear and concise, as was her habit. The Sandaime absently turned towards the wall as he considered them, drumming the fingers of his left hand as he thought.
Kekkei genkai - bloodline limits - were almost entirely confined to the various clans of the shinobi world, who guarded their unique abilities with zeal. Citizens who immigrated into Konoha had their backgrounds checked for ninja relatives - both as a precaution against infiltration and to watch for exactly this circumstance. Obviously, not every line could be traced - records missing or destroyed, orphans of war, and simply not enough time to investigate everything - and the result of such oversights was neatly documented in the scroll in front of him. A child born out of the blue with such an ability was almost unheard of.
"How was the bloodline discovered?"
"Complications during the birth. Both mother and child required healing with medical jutsu. One of the trainees noticed unusual chakra pathways and structures in the baby's nervous system. The team leader was unable to identify the cause and requested the aid of an ANBU agent."
"Has an identification of the bloodline in question been made?"
"I have tentatively identified the kekkei genkai in question as the Museigen no Shikou. The clan in question no longer exists - destroyed decades before the founding by the Uchiha, among others."
"I trust your judgment. The parents, and the baby?"
"The medics were unable to save the mother. The child will need intensive care over the next few days. The father is aware of this, but not the surrounding circumstance."
Hiruzen sighed. "What do you know of the father?"
"Haruno Kizashi, a civilian merchant. He is native to the village. I believe he is a loyal and relatively ordinary citizen."
"Who is no doubt wholly incapable of raising a child with resurgent bloodline abilities."
The masked kunoichi remained tactfully silent.
"Do you have anything further to add?"
"No, Hokage-sama."
The Sandaime sat silently for a few minutes in thought. The emergence of a new kekkei genkai in Konoha was a prize to be reckoned with. Minor wars had been fought over less. If the brief summary Panther had found describing the bloodline was correct, the baby could no doubt grow to become a powerful ninja. In another two generations Konoha might even gain another clan. The choice before him was stark.
A civilian such as the father could not deal with raising the baby. He would have no experience with the abilities his daughter would manifest, and no training to prevent injury to her or himself if anything went wrong. Civilian parents could and did raise children who grew into successful shinobi, but rarely did ninja from such backgrounds enter the elite ranks. Children with kekkei genkai, almost by definition, were born into the clans.
Sighing again, he made his decision. "The nature of the child is to be kept secret. Any further reports will be given to myself verbally. Destroy the relevant records and replace them with fakes."
"Yes, Hokage-sama."
He closed his eyes. Minato, forgive me. I fear I have failed to protect your son. Now, I will take another child from her father. Such were the burdens of leadership. Hiruzen dearly wished he could have stayed in retirement, free from the responsibilities of the Hokage. Of course, that choice is not mine to make. It was never mine to make. Who else could shoulder his burden? Tsunade had abandoned the village. Danzo? Orochimaru? His former teammate and student were both capable and extremely intelligent, but neither man valued the Will of Fire or particularly cared for the citizens of Konoha. Danzo would see us at war again within months, and Orochimaru spends all his time in the laboratory. Jiraiya's capabilities as a field agent and spy were too valuable to chain him to the village, and he had no interest in taking the Sandaime's place. Once again, Hiruzen felt the loss of his chosen successor keenly. Damn the Kyuubi.
He brought his focus back to the present. He could afford to be mournful later, when the village had no urgent need of him. Eyes hardened, the Sandaime spoke with grim finality.
"Panther. Until such time as a guardian can be found, you will be responsible for the child's safety. Have her transferred to the secure wing of the hospital. Make the necessary arrangements for the father. The medics tragically failed to prevent the death of the baby along with the mother."
"Understood, Hokage-sama."
"Dismissed."
A quick pulse of chakra released the seals, and Panther slipped out the window and flickered away. Hiruzen stared at the report again, committing its contents to memory. A quick fire jutsu turned the scroll to ash in his hand. Another wave of his hand closed and sealed the window.
Another day as Hokage. Another secret to keep. Another child to hide and protect.
Hopefully, Panther could piece together some records on the training necessary to control this bloodline. Many of the clans that had joined the village kept records back to the Warring States Era. Among these were analyses of the various abilities used by enemy shinobi - all the information that could be learned, bought, or stolen. That ANBU records were already able to match a specific bloodline to the child was promising.
Promising. Bah. A few minutes ago I was hoping for positive news. Now it has come, and I am only more regretful. For fear of an unknown bloodline, he had ordered a newborn taken from her remaining family. To strengthen Konoha, he would see her trained as a ninja, another living weapon to wield against the enemies of the Land of Fire. Konoha was often viewed as soft and weak by the other villages. Hiruzen knew such claims were nonsense. Just because the shinobi bearing leaves on their headbands did not generally attack civilians or pillage and rape in wartime did not mean they did not live according to the same brutal calculus as the others. Danzo thinks me a fool. I think he has made hard choices for so long he has forgotten that sometimes there are softer options. But when the chips are down, are we so different?
What he had ordered done tonight was wrong. In the service of the village, perhaps, but still reprehensible.
Such was the burden of the hat he had accepted. Such was his duty.
For the third time that night, Hiruzen mourned the death of Namikaze Minato. Perhaps the Yondaime, with his keen intelligence and firm moral foundation, could have found a better solution. Perhaps, perhaps, perhaps. The Sandaime, forced to retake the position he had eagerly relinquished, could not afford to take chances.
Certainly, a civilian father was not an insurmountable barrier. The situation could be explained, shinobi could be appointed as watchers, and difficulties might be managed. But such solutions would require attention and effort the village did not have to spare. It was simpler to tell the man his daughter was dead and place his daughter with more capable ninja. Simpler to cut away the complications regardless of the morality of the decision.
Simpler, to do what was easy instead of what was right.
A/N:
As many commentators have pointed out, in canon Sakura is older than Naruto. Research flub on my part when writing the first chapters, and at this point I'd have to rework a lot of stuff to fix it. So I'm going to call it another minor AU change and leave it at that.