Chapter 46 – The Death of Danzo
ROOT Division Headquarters, Konohagakure – First Basement Floor
Deep beneath the village of Konohagakure, in the underground base of the ROOT Division, more than a dozen masked shinobi stood in silence within the dimly lit entrance hall.
Hatake Kyūjō stood before them—calm and unhurried. His arms rested naturally at his sides, and his expression was unreadable as he gazed at the ROOT members without the slightest hint of tension.
But behind that serene gaze, the perceptual field of Infinity had already locked onto Shimura Danzo's position six floors below.
When the number of ROOT shinobi reached twenty-four, one of them—wearing a fox mask—stepped forward, his voice laced with suspicion.
"Hatake Kyūjō–Jōnin, why have you broken into the ROOT Division headquarters? As a captain of the ANBU, you should know that ROOT is a secret unit authorized by the Third Hokage-sama and led by Shimura Danzo-sama!"
"And more importantly… you've killed one of our own! What is the meaning of this?!"
Kyūjō didn't respond. His sharp blue eyes remained locked on them—and in that split second, lightning flared in their depths.
Without lifting a finger, he cast a Genjutsu that subtly hijacked the chakra flow through their neural pathways. In an instant, all the ROOT shinobi froze where they stood.
His voice was steady. Unemotional.
"From this moment on, the village has no further need for ROOT. Call out every last one of your members. In ten minutes… I will level this place."
"Yes, Kyūjō-sama."
Over twenty ROOT shinobi answered him in a trance-like monotone and swiftly moved to carry out his command.
As they scattered, Kyūjō's figure blinked out of existence.
— — —
ROOT Division – Sixth Basement Floor, Danzo's Private Chamber
Far below, Shimura Danzo sat alone in his private chamber, reading a highly classified scroll with intense focus. It was a copied fragment of the "Sealing Arts Compendium"—the sacred jutsu tome authored by his old mentor, the Second Hokage, Senju Tobirama.
How did such a copy even exist?
Of course… it was Danzo's doing. Back when he held significant power in the village, he'd secretly transcribed it without permission.
Even now, with the stolen scroll in hand, he found the contents maddeningly complex.
Too intricate!
Danzo grumbled to himself. Why couldn't Tobirama-sensei have developed forbidden jutsu that were simpler to learn?
The scroll was packed with powerful techniques, but only a few were actually usable… and even fewer that Danzo had mastered.
Suddenly, a voice rang out in the room—a place that should have been sealed from all intrusion.
"Having trouble, Danzo? Why don't you let me take over…?"
In an instant, Hatake Kyūjō materialized beside him, effortlessly plucking the scroll from his hand.
Danzo's eyes widened in shock. He stared at the silver-haired, blue-eyed youth standing right next to him. Before he could react further, he leapt backward, forming a hand seal as he prepared to counterattack at any moment.
"Y-You're Hatake Kyūjō! What the hell are you doing here?!"
His voice trembled with suspicion. A thousand grim scenarios raced through his mind.
Kyūjō tucked the scroll into his cloak and replied flatly.
"Hmph. Old man, thanks for the parting gift. A whole book of forbidden knowledge—how thoughtful. Still can't figure out why I'm here?"
Danzo's face twisted in fury. No one in Konoha had dared speak to him like that in decades.
"You insolent brat! Do you even understand who you're talking to?! I am the Hokage's advisor! The supreme commander of ROOT! Return that scroll at once!"
Kyūjō merely shook his head.
'Still thinks rank means anything to me, huh?'
He sighed inwardly. In a way, it wasn't entirely Danzo's fault. The old man had never truly understood the extent of Kyūjō's power.
Unlike his older brother, Hatake Sakumo—who had been brainwashed by the so-called "Will of Fire" and would sacrifice himself for the village's harmony—Kyūjō was not that kind of man.
— — —
Without another word, Kyūjō vanished from his spot.
In the blink of an eye, he appeared directly in front of Danzo.
For someone like him, Kyūjō didn't even need to use Haki. His body, still in Sage Mode, was overflowing with Senjutsu Chakra. He funneled it into his fist without hesitation.
With a quiet shimmer, a glowing iron punch shot forward—elegant, yet unstoppable—aimed straight at Danzo's forehead like a meteor descending from the sky.
"Shiki Fūjin no Jutsu!" (Four Symbols Sealing Technique)
Danzo had been prepared. He instantly activated the sealing formula embedded deep in his body—a forbidden jutsu passed down not by Tobirama, but by Mito Uzumaki, the First Hokage's wife.
Why was it considered forbidden? Perhaps due to its immense chakra cost.
In canon, even the Nine-Tails was sealed with this technique. It was that powerful.
But Danzo had long since customized the jutsu. He'd embedded a special formation in his body that allowed for instant activation, turning it into the Reverse Four Symbols Sealing, capable of sucking in everything within a massive radius… at the cost of his own life.
Yes, in the anime, Danzo used this very jutsu to commit suicide.
But here, facing a technique that could seal a Tailed Beast, Kyūjō's eyes remained calm.
His glowing fist never slowed.
The air shimmered as dark sealing symbols formed a barrier in front of him.
Then—
A sharp crack echoed through the chamber.
The sealing formula—meant to contain the Nine-Tails itself—fractured like glass beneath the force of Kyūjō's iron punch.
And without losing any momentum, his fist crashed into Danzo's skull.
A gruesome crunch of flesh and bone resounded.
In an instant, Shimura Danzo—the Hokage's advisor, the leader of ROOT—was dead. Killed with a single blow.
"Fire Release: Fireball Jutsu."
Without skipping a beat, Kyūjō channeled Senjutsu Chakra into his lungs and expelled a massive fireball from his mouth.
The flames devoured Danzo's corpse, turning him to a pile of charred ash in seconds.
Scattered ROOT members tried to resist, but to Kyūjō, they were nothing more than background noise.
In a matter of minutes, the entire underground base had been purged.
Once the last living ROOT agents were dragged to the surface, Kyūjō kept his word.
He raised one final iron fist—and brought it crashing down.
The entire ROOT headquarters caved in with a thunderous collapse, reduced to a massive crater.
Still not satisfied, Kyūjō weaved a hand seal.
"Earth Release: Earth-Style Wall."
With a deep rumble, earth and stone surged upward, filling the crater and burying the ROOT base forever.
A chapter of shadow and corruption came to a close.
And the name Shimura Danzo… was erased from the Hidden Leaf's future.
— — —
After reducing the ROOT headquarters to rubble, Kyūjō brought nearly a hundred ROOT operatives—still under the effect of his Genjutsu—to the ANBU base and handed them over to his older brother, Hatake Sakumo.
Many among them had been forcibly conscripted by Danzo. Some were brainwashed. Others carried the cursed seal etched onto their tongues—the Cursed Tongue Eradication Seal.
If there was a way to save them, Kyūjō would try. If not... then they would be judged according to the crimes in their records.
As for the two remaining village elders—Koharu Utatane and Homura Mitokado—Kyūjō decided not to move against them just yet.
If all the top officials were purged at once, who would be left to run the village?
Besides, the Third Hokage, Hiruzen Sarutobi, hadn't officially retired yet.
While the two elders were certainly power-hungry, at the very least, they still had some sense of morality. They weren't like Danzo.
Kyūjō planned to force them into early retirement. They'd receive standard pensions as ordinary shinobi, but would be banned from interfering in village policy or politics of any kind.
Unless, of course, further criminal evidence surfaced.
— — —
When all was said and done, Kyūjō sat down with his older brother, Sakumo, to discuss a new direction for the village's leadership structure.
As someone with a modern mindset, Kyūjō felt that the old system was hopelessly outdated—riddled with corruption and inefficiency. So, he proposed a full-scale reform: a complete overhaul of the village's administrative framework.
The brothers talked late into the night.
At the end of their long discussion, Sakumo looked at him sincerely and asked:
"Kyūjō… why did you nominate me to be Hokage? Why not take the position yourself? Honestly, if you were Hokage, I believe this village would thrive far more under your leadership."
Kyūjō smiled faintly and replied,
"I never wanted to be Hokage. But if you take the role, then you'll truly be able to work for the people. My job is just to offer the blueprint. In the end, truth can only be tested through action."
Sakumo gazed warmly at his younger brother. But Kyūjō wasn't done yet.
"Nii-san… I've been thinking. Back when he was young—before he became Hokage—was the Third like you?"
"Was he the type of person who would've thrown himself into the flames for the sake of the village?"
"Then why… why did he change so much?"
"Why is he now so hesitant… so weak? He let Danzo run wild. And maybe—just maybe—he silently approved of everything Danzo did…"
"Danzo committed so many crimes. You've heard it directly from the ROOT members, haven't you?"
Sakumo nodded heavily.
It was true. Some of Danzo's actions may have brought temporary benefit to the village…
But his sins outweighed everything.
He'd assassinated fellow shinobi in secret—just because they refused to submit to him.
He'd orchestrated fake missions that led to the deaths of innocents.
Even their own parents—Hatake Fūka and Yamanaka Suzune—were believed to have died in one of those staged missions under ROOT's manipulation.
But perhaps the most painful truth of all—
Hiruzen knew.
He knew it all.
And yet, Danzo received nothing more than a slap on the wrist.
Meanwhile, the two brothers had to grow up without parents…
— — —
And they weren't the only ones.
There were forbidden human experiments, the desecration of the First Hokage's corpse to extract Mokuton and Senju DNA, testing on clans with Kekkei Genkai and secret techniques…
The list of atrocities committed was long enough to erase the Shimura clan from history itself.
Sakumo couldn't even bring himself to declassify everything. Instead, he sealed the full records as top-level confidential files.
Kyūjō ended their conversation with a quiet, almost whispered voice.
"Nii-san… do you really think the Third Hokage didn't know all of this?"
"I think he knew. He just… chose not to act."
"Maybe he's just old. Maybe he lost his ideals somewhere along the way."
"…Let's just hope you never end up like him."
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