Shisui Uchiha stood at the edge of the battlefield, half-shrouded in mist and shadow. His body had fully reformed, though it still pulsed with ethereal energy from the dimension of the Sage. The Kagegan—his new evolution of the Sharingan—flared quietly beneath his brow, observing chakra flows that had long remained invisible to mortal eyes.
The forest was silent. No crows. No crickets. Just ash from a battle long ended.
He knelt and placed his hand to the ground. The soil still retained the residual warmth of jutsu. He saw it—ripples of distorted chakra, impressions in the earth. This was no ordinary fight. The air reeked of altered senjutsu.
More importantly… his own chakra signature was here.
From someone else.
Shisui rose. "A clone?" he whispered to himself, but the Kagegan refuted the thought. This wasn't a shadow clone, nor any simple genjutsu residue. It was something older. A mimicry of form that extended beyond physical.
The Sage's warning echoed in his memory:
"The world has not yet seen the final shape of chakra. And some seek to wield your face for their own ends."
He turned to the north. There, a faint trail of chakra lingered in the air—pure white, with veins of writhing darkness. Familiar and foreign. It spiraled outward like smoke in water, leading toward the Valley of the End.
With no hesitation, Shisui vanished.
---
The land warped around him as he body-flickered through valleys and cliffs. As he moved, fragments of memory surfaced. The massacre. Itachi's eyes before he fell into darkness. Danzo's grip on the Sharingan. The moment his own body faded into the waterfall's depths—eyes stolen, legacy forgotten.
No more.
The world had changed. Naruto had become Hokage. The village had entered an era of peace… but at what cost? Chakra was growing unstable in pockets. Dimensional rifts whispered of Kaguya's residual influence. Strange resurrections occurred far too often.
And now, someone walked with his chakra.
The trail led him to a smoldering temple. Bodies lay scattered—masked shinobi wearing the sigil of Root.
Danzo's men.
Still?
Shisui narrowed his eyes. The organization had supposedly been dismantled after Danzo's death, but old roots ran deep.
He descended into the battlefield and surveyed the corpses. Clean kills. Efficient. Yet not by his hand. They bore no genjutsu trauma. No signs of his signature techniques.
He paused at one.
Its chest was hollowed out, not by force, but by decay. The body had been a puppet—flesh animated by chakra strings, reinforced with cursed seals and blood-based jutsu. A mockery of life.
The kind of experiment Danzo once commissioned in secret.
Then he heard it. Breathing. One remained alive.
He turned swiftly and found the survivor—barely clinging to life, propped against a broken column.
"Uchiha..." the shinobi gasped.
Shisui knelt beside him. "Who sent you?"
The man's eyes rolled, and blood bubbled at his lips. "You... You're supposed to be dead..."
Shisui grabbed his collar. "Answer me!"
But the man's chakra flared—self-destruction jutsu. Shisui barely had time to leap back before the body exploded in a burst of flame and shadow smoke.
Too late to save him.
But not too late to understand.
In the smoke, a face formed.
His own.
But warped—his eye patterns reversed, his smile twisted.
And behind those eyes… the Rinnegan.
Shisui's heart pounded. "No..."
A clone. Not physical. A projection.
The smoke-being laughed, its voice hollow and echoing. "You left behind your corpse and your name. We reclaimed both."
Shisui activated the Kagegan. Time slowed. He could see the chakra threads in the smoke—a complex weft of yin-yang release, fueled by residual fragments of the Ten Tails and tied to spiritual anchors from beyond this realm.
"Who are you?" he demanded.
The smoke form tilted its head. "You should ask your Sage that."
Then it vanished.
Shisui remained still. Silent. The fires died around him, and the wind whispered secrets he couldn't quite grasp.
There were forces at play far beyond the manipulation of nations.
Someone had found a way to weaponize legacies.
And his was first.
---
Night had fallen fully now, casting the world in a cold indigo hue. The stars blinked overhead, indifferent witnesses to the gathering storm.
Shisui walked beneath the shadowed canopy of an ancient forest, following a trail only his Kagegan could perceive. Threads of chakra led toward a cliffside shrine, long forgotten by the world.
The temple was cracked and overgrown, its threshold bearing the seal of the Root of Shadows—six tomoe circling a void.
He pressed his palm to it. The stone warmed—not from chakra, but from intention. The door opened.
Inside was no scroll or relic. Just a pedestal. And atop it, a mask.
Old. Lacquered red. A twisted smile. A spiral of black across its face.
It pulsed with memory.
Shisui reached for it.
And the shadows recoiled.
The mask spoke—not in words, but in broken memories. Screams. Danzo's ambition. Uchiha blood spilled in secrecy. Konoha's foundation, soaked in silence.
"You were never meant to vanish," said the Sage's voice, echoing in his mind.
He dropped the mask—but it didn't fall. It hovered, tethered to his soul.
Behind him, a figure stepped from the dark.
Clad in crimson robes. Puppet-like. Familiar.
Danzo.
Or a shadow of him.
"You were always the ideal tool," the specter rasped. "Now, you will be our vessel."
The shadows screamed.
Shisui stepped back—but the door had sealed behind him. The room grew cold. The mask floated toward his face.
And the eyes in the smoke watched, waiting for him to choose.
To vanish once more—
Or to rise.
---
Shisui stood frozen. The mask hovered closer. The puppet-Danzo advanced, the air thick with manipulated chakra. Not real—but dangerous.
"You fed the fire," Shisui whispered. "You wanted peace through chains."
"And you tried to stop me," Danzo's shadow said. "Look what your mercy bought the world."
The walls trembled.
Shisui reached for his blade—but stopped. The Kagegan revealed something deeper. The puppet was tethered to another source—someone remote, watching.
A seal tag: Kinkaku Enclosure.
Forbidden soul-anchor jutsu.
Shisui stepped forward, eyes burning. "I won't wear your past. But I'll carry your mistakes forward."
He summoned shadow kunai—dozens. They spiraled into the air and struck the puppet's limbs, locking its motion.
He stepped to the seal and whispered, "Release."
The puppet collapsed.
The chakra dispersed.
The mask lay inert. Still smiling—but no longer alive.
Outside, dawn was rising.
And far away, a hooded figure smiled. "He chooses resistance. Good."
The Root of Shadows would rise.
---
Shisui moved across the terrain. Each step careful. He couldn't risk being seen. Too much had changed.
He needed answers.
He summoned a raven, embedding a sealed message. "For Naruto only."
The bird flew.
Hope stirred.
But elsewhere, deep beneath the surface, the remnants of Root experiments began to stir.
Tanks hummed.
Humanoid figures hung in suspended animation.
"Awaken the Eyes of Smoke," said a voice. "We begin the reclamation."
The war had never truly ended.
It had only waited.
---
That night, Shisui paused near a stream. The moon stirred memory.
He closed his eyes.
Under a sakura tree, Itachi sat beside him—young, innocent.
"You always disappear," Itachi said. "Like smoke."
"Smoke is shadow learning to fly," Shisui replied.
"You think that's good?"
"I think someone has to protect the light... even if it means becoming the shadow."
Itachi was silent. But something had taken root.
Now, decades later, Shisui opened his eyes.
"I'm still here, Itachi. Just in the smoke."
And then he vanished.