The village of Konoha thrummed with life. Shopkeepers called out the last of their wares, children darted through narrow streets with laughter trailing behind them, and shinobi returned from missions, their sandals scuffing against worn stone. It was a picture of peace, of order—the kind of peace so many had died to protect.
But peace is only what lies on the surface.
Beneath it, in the cracks of light, shadows stirred.
A Routine Mission
Our team had just completed another minor task—an escort duty that was more walking than fighting. It was supposed to be uneventful. In fact, it almost felt like we were being given these smaller missions to recover from the ambush.
Obito grumbled the whole way back. "Seriously, carrying supplies again? We're shinobi, not delivery boys!"
Kakashi didn't even look back. "Maybe if you trained harder, they'd give us something more dangerous."
Obito bristled, opening his mouth to argue, but Rin stepped between them, her soft voice cutting through the tension. "Enough. Missions like these matter too. Supplies keep the village running."
I walked a little behind them, letting their words drift over me. On the surface, it was a normal day—Kakashi being cold, Obito being loud, Rin keeping the peace. Normal.
But my system whispered otherwise.
[Analysis Module Active]
[Environmental Anomaly Detected.]
My eyes flicked to the left. Just for a second, I thought I saw a figure on a rooftop. A mask gleaming faintly in the dying sunlight. But when I blinked, it was gone.
I tightened my grip on the package I carried, forcing myself to keep walking.
The Quiet Street
After the report was handed in at the mission office, the team began to split. Rin excused herself, heading home. Kakashi muttered something about extra training. Obito lingered beside me, clearly torn between food and pride.
"You want to grab something to eat?" he asked, trying to sound casual.
I shook my head. "Not tonight."
He frowned. "You're acting weird lately. You—"
"Obito," Kakashi interrupted from up ahead. "Don't waste your time. He's probably just going to train too."
Obito scowled, muttering curses under his breath before storming off.
And just like that, I was alone.
The street grew quieter the further I walked. The chatter of the market dimmed, replaced by the hollow whistle of wind threading through the alleys. My footsteps echoed louder than they should have.
[Warning: Observation Detected.]
My pulse quickened.
I didn't look around immediately. Instead, I slowed, pretending to adjust the strap on my pack. My eyes flicked upward—there.
A figure. Masked. Standing at the edge of a rooftop, unmoving.
My breath caught. Not ANBU—the mask was too plain, too stripped of identity. A Root operative.
He didn't move. He didn't hide. He just watched.
The seconds dragged on, heavy as lead. Then, without warning, he was gone. No sound, no blur of motion—just gone, as if the shadows had swallowed him whole.
Layers of Shadow
I continued walking, every nerve taut. At first, I thought maybe it was just the one. A single operative sent to observe. But then—
Another. On the opposite rooftop, barely visible against the dusk.
Another. A flicker of movement behind a tree.
Another. A silhouette at the end of the street, standing perfectly still until I blinked—and the space was empty again.
They weren't attacking. They weren't speaking.
They were surrounding me.
I clenched my fists. Why? Why just watch?
The villagers passing by noticed nothing. To them, I was just another boy walking home. But I felt it—the heavy, suffocating weight of eyes in the dark.
The Hokage's ANBU protected the village. They moved unseen, yes, but their presence carried reassurance, a sense of safety.
Root's presence was different. It was suffocating. Cold. Like a hand tightening around your throat—not killing you, but reminding you it could.
The Silent Message
By the time I reached home, my nerves were frayed. I slid the door shut, leaning against it for a moment.
"Calm down," I whispered. "It's fine. They didn't do anything."
But even as I said it, I knew it wasn't true. Doing nothing was the point. They didn't need to fight me to make their presence known.
My eyes swept my small room, everything where I'd left it—except for one thing.
On the frame of the window, a slip of paper fluttered gently in the breeze.
I froze.
I hadn't sensed anyone enter. I hadn't heard a sound. But the note was there, waiting.
I crossed the room slowly, my heart hammering against my ribs. My fingers trembled slightly as I pulled the paper free.
The ink was clean, precise, written in a hand that betrayed no emotion.
"The Hokage's light casts long shadows. Which side will you stand in?"
I stared at the words, the silence of the room pressing in on me.
Root hadn't spoken. They hadn't confronted me. They didn't need to. The message was enough.
[Quest Progression: Root of Shadows – Stage 2 Initiated.]
[Objective: Survive contact with Root.]
I crumpled the paper, my nails biting into my palm.
Kakashi, Obito, Rin—they wouldn't understand. To them, Root was invisible, a rumor at best. This was my burden to carry.
But in my mind, the thought surfaced like a knife in water.
Nice try, old man. But I know how scheming you are.
I didn't speak it aloud. I didn't dare. But I thought it, sharp and bitter. The Hokage wasn't blind. He knew Root existed. He let Danzo build his army of shadows. And now, those shadows had found me.
Dream of Roots
That night, sleep came fitful.
When it did, I found myself standing in a vast field. A great tree towered above, its branches reaching for the sky, leaves shimmering with sunlight. It was beautiful—until I looked down.
The roots were monstrous. Black, gnarled, they spread endlessly beneath the earth, choking the soil, strangling every blade of grass.
One root uncoiled, thick and serpentine, wrapping around my wrist. I tried to pull back, but it tightened, dragging me down into the dark.
The sunlight vanished, swallowed by the shadows.
I gasped awake, sweat beading my forehead, my breath ragged. On my desk, the crumpled note still sat, silent and accusing.
Root had made its move. Silent. Patient. Unstoppable.
And I knew this was only the beginning.
Author's Note
Hey everyone 👋
This chapter was expanded to really push the feeling of Root's shadowy presence. Instead of just one silent operative, the MC was surrounded by watchers—none of them attacking, just reminding him he's under constant surveillance. That's Root's style: intimidation through silence, pressure through invisibility.
Highlights of this chapter:
Konoha's normal peace contrasted with MC's paranoia.
Root's multiple shadowy figures, appearing and vanishing like ghosts.
The note, left behind without a sound.
The dream sequence, foreshadowing Root's spread under Konoha.
Next chapter will focus on how MC handles this knowledge alone while the team continues training and taking missions—unaware that Root has its eyes fixed squarely on him.