Outskirts of Konoha – ROOT Stronghold
Beneath a nondescript forest clearing, hidden by illusion and buried under layers of chakra suppression seals, lay the true heart of the most shadowy part of Konoha's military machine—the ROOT stronghold.
It was a colossal underground fortress, a labyrinth of cold stone corridors, armory vaults, observation rooms, and sealed chambers designed for interrogation, experimentation, and indoctrination.
Here, the truth was discarded. Morality, an inconvenience. Only one thing mattered: Konoha's survival. Or so its commander claimed.
And yet, in Konoha's hour of need… ROOT did nothing.
As the village burned and shinobi bled in the streets, ROOT was silent.
But not everyone had forgotten them.
Above the surface, shrouded in black cloaks to obscure their chakra signatures and identities, a small, elite unit stood silently before the camouflaged entrance.
Their presence was like a loaded arrow—tension humming in the air.
"So, Tōshu, are we entering now?" one of the masked figures asked the one at the front.
He was slightly taller, stood straighter than the rest.
The one they called Tōshu nodded, eyes gleaming beneath his hood. "Yes. Naruto's signal came through. We move."
They all steeled themselves.
"And remember," he added, voice sharp, quiet, dangerous. "Minimum casualties. That's what he asked for. We're not murderers… not like them."
The team moved. Silent as smoke, fast as lightning.
The two guards at the entrance never stood a chance—a single nerve strike, a flash of chakra, and they crumpled soundlessly to the forest floor.
Not killed. Just silenced.
They slipped inside like wraiths—through pitch-dark tunnels, each step taking them deeper into the belly of the beast.
One by one, they picked off patrols and surveillance teams. Non-lethally. But efficiently.
This wasn't a bloodbath. It was a surgical purge.
ROOT Stronghold – Inner Chamber
In the deepest part of the base, beneath multiple security barriers, sat Danzo Shimura.
An old man, yes. But no less dangerous for it.
His right eye was hidden behind a thick bandage, as was his arm—sealed away to keep secrets best left unspoken. Both hands rested on his ornate black cane.
Two figures flanked him.
On his right: Fu Yamanaka, late 20s, face calm, cold, eyes always thinking two layers deeper than his words.
On his left: Sai—young, unreadable, unnervingly still. His face was like paper, blank and quiet.
Danzo's voice, when it came, was dry and low.
"...What's the situation in Konoha?"
Fu answered swiftly, fingers interlocked behind his back. "The village is under assault. Sunagakure has allied with Orochimaru. The Chūnin Exams were the launch point. Mass panic is ongoing."
Danzo exhaled slowly.
"Hiruzen?"
"Trapped. He's inside a barrier, likely fighting the Kazekage and Orochimaru simultaneously. The technique appears similar to Kekkai: Tengai Hōjin, but fused with an external containment seal. We cannot observe the battle directly."
Danzo didn't move, but his presence grew heavier, like a storm cloud coiling.
"Hmph. The fool let sentiment cloud his judgment… Again."
His fingers tightened on his cane.
"He should've removed Orochimaru long ago. He knew what that snake was capable of."
Fu tilted his head slightly. "Shall we mobilize, Danzo-sama?"
"No."
Fu blinked. "Sir?"
"We wait."
Fu's jaw tensed.
Danzo's voice was steel now. "Let the village bleed. Let it beg. Only when the people are desperate will they accept a new kind of leadership. My leadership."
Fu said nothing. Sai, like a puppet under chakra threads, simply stared ahead, unmoving.
Danzo closed his eye.
He didn't notice the faint sound—the barely perceptible silence—that was descending across his base.
The kind of quiet that only meant one thing.
Someone had entered the wolf's den.
Danzo Shimura's fingers tightened over his cane. The cold breath of instinct—a sense honed through decades of blood-soaked war and whispered betrayals—crept up his spine like a chill draft in a sealed room.
Something was wrong.
"Sai," he said, his voice calm but edged with steel. "Deploy your jutsu. I want an aerial view of Konoha immediately. We need strategic insight before we intervene."
"Yes, Danzo-sama." Sai gave a quick nod and exited silently.
"And Fu," Danzo continued, "mobilize the ROOT operatives. Prepare for mass deployment. Time to cut out the cancer while the village screams."
Fu bowed. "Understood."
They both vanished down the dark hallway.
Danzo exhaled, closing his only visible eye.
"Let's see what the future holds."
But as the door sealed behind them... silence.
Unnatural. Hollow. Not a whisper from the labyrinth beyond.
ROOT Corridors — Moments Later
Sai stepped through the main tunnel, brush in hand, already forming chakra-infused ink. He planned to summon an eagle for reconnaissance—high, fast, invisible to the untrained eye.
But something gnawed at him.
Where were the guards? The patrols? ROOT never left itself exposed.
Fu, on the other hand, moved faster—his instincts screaming. His mind connected the dots far quicker.
No sentries. No chakra presence. No movement.
This wasn't a stronghold anymore.
It was a tomb.
"Where the hell is everyone?" Fu muttered.
Then—
A flash of movement.
Too fast.
From the shadows, black-cloaked figures emerged like ghosts. Precise. Cold. Coordinated.
Fu reached for his kunai—but he was too late.
One hand gripped his wrist. Another wrapped his mouth.
Pressure point. Chakra block. Silence.
His vision blurred as consciousness slipped. But before everything faded—
He saw him.
A face thought long dead. A shadow from Danzo's past.
Shisui Uchiha.
Alive. Standing. Both eyes are intact.
Fu's world went dark with that impossible truth.
Elsewhere, Sai met the same fate—his body subdued, his last thought also burned with shock.
"How… does he have both Sharingan…?"
ROOT Inner Chamber
Danzo still sat, unmoving. Calm as ever.
He was forming a strategy—one that would allow him to seize the chaos outside and rise to the seat he always believed was his.
Click.
The chamber door creaked open.
Danzo didn't look up.
"Just in time," he said coolly. "I've decided. We make our move. Mobilize every unit. The Hokage seat is within reach—"
"So this is where you've been hiding your cowardly ass, Danzo."
The voice cut through the silence like a kunai through silk. Familiar. Deep. Male. And unmistakably full of disdain.
Danzo's eyes narrowed. That wasn't Fu. And Sai? The boy barely spoke unless commanded.
He turned, his old bones stiff, a cold dread crawling up his spine—and froze.
No. No, it couldn't be.
It wasn't Fu.
It wasn't Sai.
It was him.
The shadow Danzo believed he had erased from Konoha's history. The man whose death he had ensured.
Fugaku Uchiha.
The once-proud head of the Uchiha Clan stood in the doorway, face calm, eyes unreadable. He pulled down his hood with a casual grace.
Danzo's breath caught.
Fugaku smirked. "I like that look on your face. That 'I'm-seeing-a-nightmare-walk-in' look. Classic."
He strolled into the room like he owned it, each step echoing with authority built on decades of command. Calmly, he sat across from Danzo at the table, crossing one leg over the other.
Danzo stumbled back, his cane trembling.
"W-Who are you!?" he barked, voice cracking despite himself.
Fugaku sighed, waving a hand. "Please. Lower your voice. I've been dead for years, the ears aren't what they used to be."
Then, with a subtle tilt of his head and a piercing stare, he added, "Though I suppose this is the second time you've stared into the face of someone you were sure was dead, isn't it?"
Danzo's face went pale. Sweat rolled down the side of his temple.
Fear.
He started flashing through hand seals—old reflexes from another era.
Too slow.
Click.
Fugaku didn't even move. Just looked.
And Danzo's world twisted.
GENJUTSU — Illusion Realm
Danzo stood triumphant, sword dripping blood, over Fugaku's corpse.
Then blinked.
Fugaku stood again.
Slain.
Alive.
Slain.
Alive.
Over and over again.
A looping nightmare.
Reality
Fugaku exhaled, rubbing his fingers over the desk.
"Always so dramatic," he muttered as he skimmed the nearby scrolls and drawers. "Let's see what corruption you've been hoarding, old man."
Just then, the door opened again.
Shisui Uchiha stepped in, his presence quiet but sharp as steel. "Fugaku-san. We've secured all Root operatives. Every last one. We also recovered the documents detailing Danzo's collusion with the other council elders."
Fugaku glanced back, unfazed. "Of course, he kept records. Blackmail's his favorite form of diplomacy."
Shisui pointed to Danzo, still frozen in place. "Is he dead?"
"No." Fugaku stood. "And I won't kill him—not yet. I promised Naruto he'd live. That justice would be done publicly, not in the shadows where Danzo prefers to operate."
Shisui nodded. "Understood. Should we escort you back to Konoha?"
Fugaku adjusted his cloak. "No. You stay. Gather every document, secure every Root shinobi. Lock them up—one cell, reinforced. As for him…"
His eyes flicked to Danzo, whose body had begun to twitch—the genjutsu cracking, his chakra nearly depleted, his spirit fractured.
"…put him in isolation. Two guards minimum. Don't underestimate him. He may be old and rotting, but this man once wore the vest of an Elite Jōnin."
As if on cue, Danzo snapped out of the illusion—only to collapse to one knee. His skin was pale. His chakra flickered weakly. His eye was wide, unblinking.
Fugaku walked past him without a glance. "We'll see what the fire of Konoha's justice does to a man who's spent a lifetime hiding in the shadows."
He stepped through the doorway, his cloak billowing behind him.
Outside, the world was burning.
And Fugaku Uchiha was ready to join the fight.