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Chapter 31 - Counter Root (Not)

Time moved forward.

Weeks passed, like drifting leaves in the wind, unnoticed until they were gone. And now, only a few days remained before the next generation — including Akai and other younglings — would take their first step into the shinobi world by enrolling in the Academy.

Takahiro, as always, found his mind drifting back to the orphans.

To Root.

To what the Hidden Villages had become.

Organizations were born with ideals — always. That was their first breath: passion, vision, promises to uplift. But like rot in wood, time and power wore down those bright beginnings. Root had once been created to protect the village from the shadows. Now, it was the shadow. Feeding on the forgotten. Enslaving the broken. Manipulating the system it was meant to support.

The Hidden Villages themselves weren't immune to that decay. What had once been a pact of unity — Senju and Uchiha founding a haven for their children — had twisted into a machine where children were currency, and orphans... were assets. Discarded, collected, controlled.

Takahiro would play the same game now.

Only better.

Where Danzō hoarded power through fear and exploitation, Takahiro would build something with eyes wide open — and strike when the time came.

That was when he agreed to Nono's proposal.

He purchased the Konoha Orphanage.

Quietly. Legally. Completely.

The previous owner vanished from public records, and a new director — vetted and loyal — took their place. Funding poured in. Supplies appeared. Children were clothed and fed. But above all, the environment changed. Gentle, but intentional.

Then came the inevitable meeting.

A casual encounter within the Hokage's presence. Danzō Shimura arrived with his usual grace — which was to say, none. His dark robes moved like a specter behind the lines of bureaucracy. And he wasted no time.

"I hear you've taken a sudden interest in philanthropy, Elder Takahiro," Danzō said, his single visible eye unreadable. "The orphanage. Quite a generous investment."

Takahiro, standing with hands folded behind his back, offered the barest of smiles — the kind only the experienced would recognize as a challenge.

"I am simply softening in my old age, Lord Danzō," he said formally. "With my grandson no longer within the Hyūga compound, I find myself with an excess of paternal instinct and nowhere respectable to place it."

Hiruzen, seated behind his desk, gave a quiet chuckle, brushing ashes from his pipe. "You've always had that side, Takahiro. People just mistake your bluntness for cruelty."

Takahiro bowed his head respectfully toward the Hokage.

"You honor me, Lord Third. I would not pretend to rival your endless patience, but I do attempt to... adapt."

Danzō's expression barely shifted, but his silence grew cold.

"Still," the elder added, his tone sharpened just slightly, "it is reassuring to know that certain institutions are now under safer guidance. The wellbeing of our orphans should not be treated lightly. I am sure you would agree."

"I do," Danzō said curtly.

Yet the air said otherwise.

To Hiruzen, the exchange seemed little more than two aging men trading polite remarks. But beneath the niceties, venom pulsed — not shouted, but whispered like a drawn blade behind silken words.

And Takahiro — always the tactician — was already moving pieces on the board Danzō had long thought was his alone.

The orphanage expanded fast. Takahiro's orders were swift, exacting. He commissioned Earth-style users to carve out the deeper foundations, called in carpenters, workers, and shinobi alike. His wealth was more than sufficient—most of it untouched since the Third Great War. But beneath the stone and wood, beneath the polished halls and smiling caretakers, there lay something else.

A hidden basement. A facility.

The ceiling was low. The walls were stone. No windows. Just lamps lining the ceiling like dim stars caught in an eternal night. It was here that the children lived—children smuggled out of Iwagakure, hidden away in passageways and sealed wagons, all bearing false names and stolen papers.

"Are you the children Yakushi—no, Nanigashi sent?" Takahiro's voice echoed in the air-tight room. His Byakugan flared—not as a threat, but as a message. Authority. Control. Expectation.

He remembered. In Iwagakure, she had used an alias. Nono Yakushi was Nanigashi there—a ghost who moved between shadows, not a medic-nin but a whisper on the wind.

It had taken all of Takahiro's influence to arrange this, but he had done it. Just like that, Danzo's pipeline—the steady stream of Root-bound "tools"—was undercut. The orphanage that had once relied on Hiruzen's goodwill now belonged to a Hyūga elder. And that elder was done playing nice.

Kidnaping infants? Turning them into tools? You think only Danzo can do such a thing?! Takahiro knew, this was only the beginning.

He descended into the basement that day flanked by two loyal Hyūga chūnin, faces stiff, movements crisp. The children inside were gaunt but alert. They stared at him not with fear—but with something worse: hope.

Hope, he believed, was poison.

"These expressions of yours," he muttered. "They will not serve you."

Training began.

Harsh. Unforgiving. Unrelenting.

He barked commands, struck with chakra-coated palms, tore down their technique, their form, even their confidence. When one of the boys—only twelve—winced and dropped his kunai, Takahiro knocked it from his hand with a precision strike.

"Pick it up. Do not ever flinch. In this world, flinching gets you killed."

The kids were broken down. But not in the way he expected.

He thought they'd go quiet. Numb. Like Root's children—dead eyes in living bodies.

Instead...

"Thank you for the correction, Takahiro-sama!" one of them shouted through bloodied lips.

He blinked. "What?"

Another, a girl with her hair tied in crooked pigtails, bowed after being knocked off her feet. "Your movements are really cool, Granpa-sensei!"

"Granpa—?"

And then came the worst of them all: Urushi.

Older than the rest. Smarter. Always smiling like a damn fool. After every brutal session, he was the first to rise and the last to stop moving. He called the other kids "little siblings," and referred to Takahiro as White-Eye Chief.

Takahiro tried harder. Harsher drills. Colder discipline. But every bruise, every chakra burn, just made them more... affectionate?

They thanked him. Repeatedly.

And then came the moment of no return.

One week in, he returned for a surprise inspection. Two of the boys were pulling on a girl's hair, mocking her freckles. Before the caretakers could intervene, Takahiro stepped in.

"What is the meaning of this?"

"Uh, w-we were just—"

THWACK! THWACK! That sound was also familiar to him, he was surprised he was able to produce such beautiful thwacks like a few months ago with a certain kid he always dragged around.

Two slaps straight to the head. The boys screamed while two smokes roses from their heads.

"You shame this house. You shame yourselves. And if you think I won't personally escort you back to the womb for a second chance at development, try me."

The room froze.

And then—

"GRANPA WHITE-EYES!!" the bullied girl shouted, leaping at him and hugging his leg. "Thank you! A-also, They called me ugly!"

He stiffened. Visibly. Comically. As if his body didn't know whether to respond with a jutsu or a hernia.

She beamed. "You're the best granpa ever!"

He opened his mouth to scold her. To explain that he was here to make tools, not take in strays.

Instead, he muttered: "...tidy your collar before speaking to a superior. And stand up straight."

She nodded like he'd just revealed a secret jutsu.

....

That night, back in his study, he slammed his teacup on the table. Lukewarm. Pathetic. Just like this entire—

He paused.

His reflection on the metal kettle stared back at him. Lines deeper than last year. Beard unkempt. A faint... smile?

"...What am I doing?" he muttered.

He even attempted a basic telepathic jutsu on the children, curious to glimpse their thoughts about him. Every mind he touched bloomed with smiles and butterflies—simple, happy impressions.

The technique itself was rudimentary, relying on an inefficient structure that consumed a considerable amount of chakra to offset its lack of precision. Which made his thoughts drift back to the unsettling fact that his plan was failing.

He thought of Danzo. Of Root. Of emotionless weapons trained to kill without blinking. And yet here he was—handing out sweets and hand-me-downs.

It didn't look like Danzo's work.

It didn't feel like Danzo's work.

And maybe, just maybe... that was the point.

"Haa~ I give up." Those words were filled with smiles, and memories of the kids thoughts and smiles during training and during education hours. It's not like he always needed emotionless tools to win the war anyway.

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As always, the room was dim.

The walls were smooth, gray, and bare — like the inside of a coffin. Root's main chamber didn't need warmth. It didn't need life. Just silence.

It was connected through a latticework of tunnels hidden deep beneath Konoha, where voices were deadened and secrets crawled like insects under the skin of the village.

And at the heart of it all, sat Danzō Shimura.

He was alone. As always.

The candlelight wavered gently at the far end of the table, the flame fighting its own inevitable death. Its flickering glow cast strange shadows across the wrinkled lines of Danzō's face, making him seem less like a man and more like a carved statue, made not of stone, but of guilt calcified by time.

He seethed. Not outwardly. His breath didn't quicken. His body didn't twitch.

But his mind was a storm.

Takahiro Hyūga.

That old fossil. That self-righteous fool.

A sharp memory stabbed through his thoughts.

—A scroll. A signature. A transaction. The orphanage. Purchased outright.

It wasn't just the facility. It was the supply. His supply. The quiet pipeline of "candidates" was drying up. One after another, his threads were unraveling. And now, someone else was threading their own needle. Right through the eyes of the future.

Danzō's fingers tightened on the armrest. But it wasn't anger that made his knuckles white.

It was fear.

The one emotion that had never left him.

The same one that had been there since he was young. Since that moment.

Team Tobirama. A mission gone to hell. When their squad was surrounded and their survival was narrowing like the point of a blade.

"The enemy's too close," Tobirama had said, calm and grim. "One of us must act as a diversion."

Danzō had known then. The obvious play. One of them needed to step forward. Sacrifice. Duty. Will of Fire. All those noble words plastered on the hearts of boys too young to understand what it meant to die.

And he had wanted to be that person.

Had told himself to be that person.

His lips had opened.

But not fast enough.

"I'll do it," Hiruzen had said.

Danzō remembered cursing, quietly. But not at Hiruzen. No — he had cursed at himself. Because in that breath, between choice and silence, he had felt relief.

He had been relieved that it wasn't him.

That was the moment he understood who he really was.

Not a hero. Not even a warrior.

Just a man. A coward dressed in war paint. And he had spent every breath since trying to compensate for that moment.

He didn't deny it. What was the point? Cowardice had become his armor. His obsession with control, his paranoia, his endless scheming — they weren't born from ambition. They were born from fear. Of betrayal. Of death. Of irrelevance.

And so he had shaped Root into his answer. If he could not be brave, he would be careful. If he could not be pure, he would be effective.

Tools didn't need to be trusted. They just needed to be used.

He sent them on missions that killed them. Not because he wanted them to die. But because it was better they die under his control than live long enough to act on their doubts.

And now, he thought bitterly, even the tools are being stolen.

He rose slowly, cloak brushing the floor like trailing regrets. The silence in the room was deafening — a silence he had cultivated for decades, now turning against him. Like all tyrants, he had surrounded himself with silence until it became unbearable.

He moved to the scrolls on his desk. Maps. Names. Numbers.

But above all else...

His mind wandered back to that child.

Akai.

A perfect contingency.

A Hyūga... but not truly. A branch member. The kind the main house liked to leash like dogs and dismiss as lesser. And not just Hyūga — he carried the blood of the Uchiha too, however diluted. A convergence of two of the strongest lineages Konoha had ever seen. By all accounts, the boy should have been a political firestorm, but instead, he was a discard.

Perfect.

The thought had once thrilled Danzō.

So what if he was too old to be broken down and rebuilt from scratch like the Root operatives? So what if he had already begun to form "attachments"? That just meant he could be molded into something else — a living symbol.

A boy scorned by his branch clan. A survivor from the outskirts of nobility. Not the elite, but the scrap just underneath it — the kind the village would overlook.

Until he rose.

Under his care.

Danzō pictured it then: a dramatic scene of public heartbreak. Akai, wounded, kneeling, rejected, cast aside by his own people. 

And then... a hand, extended like the sun cutting through storm clouds. Danzō's hand. The savior of the child with dual heritage. The "darkness" giving rise to light. A phoenix from ash. A boy turned hero — shaped by Danzō Shimura.

Unlike all the other geniuses that would be cast aside as a tool, he was determined to make that one boy his eternal praises-for-elder-danzo spouting machine when the time comes when Hiruzen is killed.

It was beautiful.

He'd nurtured that vision carefully, adding layers with every passing day — waiting, preparing. All while claiming the title of "darkness" behind the leaf. Saying it to Hiruzen. To others. To himself.

"You are the light, Hiruzen. I am the shadow beneath the roots."

How many times had he rehearsed that?

It sounded noble. Righteous, even. He was the unseen sacrifice — the diseased limb amputated to save the body. The toxin that kills the parasite. The "necessary evil" in every shinobi drama.

But somewhere along the way, Danzō had forgotten something critical.

Darkness doesn't envy the light.

It simply existed beside them.

But Danzō... Danzō did envy it.

He had stared up at the Hokage Monument more times than he could count, the wind brushing over his face like a lover that would never kiss him. Watching Hiruzen's face carved into stone while his own contributions were buried underground like corpses no one visited.

And the truth clawed back to the surface — the truth he buried deeper than even Root:

He wanted the light.

He wanted the seat.

Not just to rule, but to be seen ruling.

All that talk of being "the root that supports the tree"? It was a lie to justify the rot. He wasn't the dirt — he wanted the sturdy branches, the green leaves, the crown.

And now Takahiro had dared to step into his domain.

Danzō rose from his chair, the shadows in the chamber swirling as if pulled by the tide of his resentment.

The orphanage. The children. Akai.

They were slipping through his fingers.

His "perfect plan" was unraveling, thread by thread, and he could already see the signs: Akai was smiling more often around that grumpy old Hyūga, no, it was as if he never cared about the scorn of the other branch member anymore. He even started hanging out with the Kyubi's jinchuriki, That was dangerous.

Danzō couldn't allow that.

He could feel it all slipping. The false image of nobility he wore was cracking, and underneath... was just the same man he'd always been:

A Coward.

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.

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Takahiro stood in the middle of the training ground, arms folded behind his back, face locked in that usual scowl.

Around him, the children were laughing — laughing — while running through a newly constructed obstacle course he'd personally designed to break their spirits, not brighten their day.

He clicked his tongue.

"Jump higher, fools! In a real battle, you'd have died five times over by now!" he barked.

A round of "Yes, White-Eyed Grandpa!" echoed back cheerfully. One of the younger boys even tripped over a rope, then thanked him for setting it up. Another offered him a hand-drawn picture of a grumpy man giving candy.

What the hell was happening?

This was supposed to be Root: Version Two. Not the damn Nara clan daycare.

Even in the dim, sweat-soaked air of the underground chamber, it smelled less like war preparation and more like... whatever warm, fuzzy garbage Hiruzen probably wrote in friendship scrolls back in the day.

And speaking of that man—

Hiruzen had started visiting more frequently. First it was once a month. Then biweekly. Now? Practically every few days, the old coot was strolling around the orphanage like he owned the place.

Takahiro, despite his internal screaming, bowed respectfully every time. "Hokage-sama, I hope you find the facilities adequate."

Inside, he was seething. Why is this guy here again? Don't you have a stack of papers the size of the Hokage Monument to deal with?

They'd walk through the training fields, past the study halls and dorms, exchanging words. It always started with something simple — crop yields, funding, academic scores. But somehow, the conversation always turned to Akai.

"Enrolling soon, is he?" Hiruzen mused one afternoon, hands tucked behind his back, puffing that ancient pipe of his.

"Yes, Hokage-sama. A few more days."

"Bright child," Hiruzen noted. "Though a bit of that Hyūga pride flares up now and then."

Takahiro muttered a neutral, "I shall correct it."

They kept walking. And then it came — the shift. Hiruzen mentioned the registration period for the Academy had long since passed, but Takahiro found himself pausing mid-step.

"...May I request an exception?" he asked. "There are several children under my care who are prepared to undergo the same training. They... wish to become shinobi."

Hiruzen blinked and scratched his head. "Hmm... yes, I suppose that can be arranged. But you'll have to finish all the paperwork. You wouldn't believe how my desk swells every time I so much as blink." He chuckled, his eyes squinting behind the smoke. 

"Paperwork is the true Hokage's burden."

Takahiro nodded, folding his hands behind his back.

In truth, the number of children eligible for his special training was few. The original group of Iwa illegal transfers numbered only seven. The rest of the orphanage kids either didn't want to become shinobi or had already been enrolled.

Ultimately, only ten children were part of his underground training program — what was supposed to be Danzo-style conditioning but had somehow become... parenting.

Of course, there were layers even he didn't speak aloud.

One child in particular held his attention: a boy with no surname. The quiet one who always sketched on scraps of paper — Sai.

Takahiro had taken note of him early on, especially his growing bond with an older Root operative named Shin. Most Root children were dead-eyed and mute, but Shin... Shin actually laughed with Sai. Encouraged him. Showed... care.

That, more than anything, made Takahiro uneasy. Was Shin coaxing the boy to Root? Or was he a failed project himself?

Either way, Takahiro saw to it that Sai be guided to the Academy — keep him away from Danzo's hands.

"Ten, I believe?" Hiruzen raised a brow, blowing smoke lazily. "I suppose that's acceptable. The enrollment roster's already been 'unofficially' amended anyway. What's a few more?"

Takahiro narrowed his eyes.

"...Amended?"

"Oh, right," Hiruzen said, as if recalling he'd left the stove on. "A couple of last-minute entries. Two children joined post-deadline. Special cases."

Takahiro's brow twitched.

Two?

Normal civilians wouldn't get such treatment. Not unless they had serious backing.

He turned toward the Hokage. "Who?"

Hiruzen smiled faintly, savoring the dramatic pause before he answered.

"One is the priestess from the Land of Demons," Hiruzen said. "She's here to study Ninjutsu. Her name is Shion."

Takahiro gave a small nod. That tracked—he'd heard Priestess Miruko's name often enough from the monks at the Fire Temple.

"And the other?" he asked.

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To be continued

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