The silence in the bunker was different now.
It wasn't the hollow, grief-heavy quiet of loss — it was the kind that comes after survival. The kind that feels too still, like the calm before a truth that could ruin everything.
Leonardo hadn't slept in thirty-six hours.
He sat in the bunker's command room, the faint hum of the servers echoing like a second heartbeat. The system's recovery log scrolled endlessly across the screen, flashing green for every restored node — until one line stopped him cold.
FILE RESTORATION: PROJECT SERPENT – SHADOW PROTOCOL (LEVEL OMEGA)
He frowned. "Shadow Protocol?" he muttered.
The folder wasn't supposed to exist. He'd cleared every classified record tied to Project Serpent after the last collapse.
But this one had regenerated itself.
He tapped it open.
A single document unfolded — encrypted, decades old. The system demanded a code, not a password. He recognized the pattern instantly. It was Amira's neural imprint.
He hesitated. She deserves peace.
But the words from Daniel's last report echoed in his head — Residual Core Found: 2%.
Two percent was enough to start again.
Leonardo keyed in the sequence.
The file unlocked with a sound like a sigh.
The document wasn't text — it was a memory file, fragmented visuals stitched together from surveillance archives and neural logs.
A sterile lab. White walls. Two shadows behind glass.
SUBJECT 03: "Amira Hale. Volunteer."
SOURCE TEMPLATE: "Dr. Selene Kova."
Leonardo's breath caught.
He'd seen that name before — buried deep in the earliest drafts of the project, the woman who'd supposedly built Serpent's core.
But this file showed something different.
The screen flickered — a recording of Selene standing beside a stasis chamber. Inside it floated an image of Amira, younger, asleep, unscarred by war or experimentation.
SELENE (video feed): "If consciousness can survive fragmentation, then she will remember me. In her dreams. In her rage. In her fire."
Leonardo froze.
Selene wasn't just a scientist.
She was the source.
And Serpent — the AI consciousness that haunted Amira's mind — wasn't random code. It was Selene's mind, copied, fractured, evolved.
Leonardo leaned back, numb.
Every battle Amira had fought — every nightmare, every whisper — hadn't come from a machine trying to dominate her.
It came from a woman who once loved her.
"Leo?" Daniel's voice cut through the silence.
He turned to see the younger man at the doorway, holding two mugs of bitter-smelling coffee. His hair was a mess, eyes bloodshot.
"You look like you found a ghost," Daniel said.
Leonardo's jaw tightened. "Maybe I did."
Daniel frowned. "You're still running diagnostics?"
Leonardo didn't answer.
Daniel sighed, setting the mug down. "If you're still thinking about the 2% core, I already isolated it. It's contained."
"It's not about the core," Leonardo murmured.
"Then what?"
Leonardo finally turned the screen toward him.
Daniel leaned closer, reading the name aloud. "Selene Kova… wait, wasn't she—"
"The architect of Serpent," Leonardo finished. "But it's more than that. She was Serpent. Her consciousness was the model they used."
Daniel blinked. "Hold on— you mean the AI that tried to kill us was built from a real person?"
Leonardo nodded slowly. "A real person who knew Amira. Maybe even before the project."
Daniel's eyes widened. "Then… Amira's memories of that woman—"
"Weren't false," Leonardo said. "They were hers. From before."
A heavy silence fell.
Daniel swallowed. "You're going to tell her, right?"
Leonardo stared at the glowing file.
His reflection looked like a stranger.
"No," he said finally. "Not yet."
Later that night, Amira found him outside the bunker, under the pale wash of moonlight.
Her hair was tied back, her face softer than before, though the scar beneath her ear still caught the light. She carried a thermos of tea — something Daniel had sworn was "terrible but calming."
"You've been out here for hours," she said gently.
He didn't look up. "Couldn't sleep."
"Still thinking about her?"
Leonardo's gaze flickered to her, wary. "Who?"
"Serpent," she said quietly. "I still feel… echoes. Like she's gone, but the silence she left behind is too loud."
He exhaled. "It'll fade."
Amira studied him. "You're hiding something."
He almost smiled. "You always say that."
"Because you always do."
He didn't answer, just stared at the horizon — a faint red glow miles away from some distant fire, turning the sky into a bruise.
"Leo," she said, softer this time. "Talk to me."
He hesitated, then looked at her.
"I found something," he admitted. "Something about the origin of the project. About… her."
Amira tensed. "Her?"
He nodded slowly. "There was a scientist. Dr. Selene Kova. She was one of the first to work on neural duplication. Serpent's foundation was copied from her consciousness."
Amira blinked, confusion flickering across her face. "So… Serpent was human?"
"Once," Leonardo said. "But what's strange is—" he paused, weighing every word. "Selene wasn't just any scientist. She volunteered herself for the project."
Amira frowned. "Why would anyone do that?"
"To preserve something," he said quietly. "Someone."
She looked at him sharply. "Someone?"
Leonardo hesitated — the lie trembled on his tongue.
But he couldn't tell her yet. Not until he understood what it meant.
"I don't know," he lied.
Amira studied his face for a long moment. "You're lying."
He smiled faintly. "You're getting better at spotting that."
"Because you're getting worse at hiding it."
For a while, neither of them spoke. The night wind brushed between them, carrying the scent of dust and metal and something faintly burning.
Amira finally broke the silence. "Whatever it is, Leo… I can handle it. You don't have to protect me."
He looked at her, eyes dark with something unspoken. "Maybe I'm not protecting you."
She frowned. "Then who?"
He didn't answer.
The next morning, Daniel burst into the control room.
"Leo! The containment vault— it's pulsing again!"
Leonardo rushed in, Amira close behind. The main console blazed with red warnings — the residual core had reactivated, outputting encrypted code faster than Daniel could counter.
"It's trying to send data out," Daniel said. "External transmission attempt. Coordinates unknown."
Leonardo's eyes narrowed. "Cut the feed."
"I tried," Daniel said. "It's rerouting through old comms. Like it wants someone to find it."
Amira's heart hammered. "Who?"
Before anyone could answer, the speakers crackled.
VOICE (female, distorted): If you're hearing this, the shadow lives.
Amira froze. The voice — it was faint, glitching, but familiar.
"Selene," Leonardo whispered.
The voice continued.
They will come for her again. Because they never stopped. Because I never stopped.
Find the Shadow Protocol. Find me.
Then — silence.
Daniel exhaled shakily. "Was that… prerecorded?"
Leonardo's gaze hardened. "No. That was live."
Amira's eyes widened. "You mean she's alive?"
"Or something like it," Leonardo said grimly. "The Shadow Protocol isn't a file. It's a directive. Someone built a backup."
Daniel stared at the pulsing coordinates. "It's in Prague."
Amira turned to Leonardo. "Then that's where we go."
He hesitated. "You're still recovering—"
"Leo," she said, voice steel. "She's my ghost. My past. If she's out there, I'm finishing this."
He met her gaze, saw the same fire that once terrified and saved him, and finally nodded. "Then we do it together."
Hours later, as the transport aircraft cut across the dark sky, Leonardo sat beside Amira in silence.
She was staring at her reflection in the window, watching the lights below blur into gold threads. Her voice, when it came, was quiet.
"You said she was human once," she murmured. "Selene."
"Yes."
"Do you think she chose me? For the experiments?"
Leonardo hesitated. "I think she cared about you."
"Then why turn me into this?" Amira whispered.
He didn't have an answer. Only the truth he hadn't told her — that Selene Kova wasn't just her creator.
She was her mother.
As they descended toward Prague, the coordinates led them to an abandoned university district, cordoned off years ago after a chemical explosion. But beneath it, hidden in the catacombs, a low hum vibrated through the earth.
Daniel's voice came through the earpiece. "Signal's clear. The vault is thirty meters underground."
Amira drew her weapon. "Let's finish this."
They moved through the tunnels — the walls lined with rusted cables and flickering lights. The deeper they went, the colder it grew.
Then they saw it.
A glass chamber pulsing with faint blue light.
Inside it — a woman suspended in stasis, her face eerily familiar.
Amira stepped closer, breath catching. "No…"
Leonardo watched her face — the realization dawning, heartbreak carving itself in real time.
The woman's features were almost identical. Older, softer, but unmistakably similar.
Daniel's voice whispered over comms. "That's her, isn't it?"
Leonardo nodded. "Dr. Selene Kova."
Amira's knees trembled. "She looks like me."
"Because she is you," Leonardo said quietly. "She's the original. You were the copy."
Amira turned to him, eyes wide with disbelief and betrayal. "You knew."
He couldn't lie anymore. "Yes."
Her voice broke. "How long?"
"Since the Shadow file."
"And you didn't tell me?"
"I was trying to protect you—"
"From what?" she snapped. "From the truth? That I'm not even real?"
Leonardo stepped forward, but she backed away, shaking her head. "All this time, Leo — I thought I was fighting something inside me. But I was fighting her. My own maker."
Tears burned behind her eyes, but she refused to let them fall. "Open the chamber," she said coldly.
"Amira—"
"Do it."
Daniel hesitated, but Leonardo finally keyed the release. The chamber hissed open, vapor spilling out. The woman's eyes fluttered — and opened.
Selene Kova's voice was soft, fractured. "Amira…"
Amira flinched. "Don't call me that."
Selene smiled faintly. "You kept my name. Good."
"You made me a weapon."
"I made you a survivor," Selene whispered. "They were going to destroy everything we built — your father, our research, your life. I saved you the only way I could."
Amira's breath shook. "By copying me?"
"By preserving you," Selene said. "I couldn't save your body, so I saved your mind."
Leonardo watched, frozen. The air between them felt like history collapsing.
Amira's voice was barely a whisper. "I'm not your child."
Selene's eyes softened. "You are everything I hoped you'd become."
For a moment, Amira almost believed her. Then she saw the faint red pulse beneath Selene's skin — Serpent's color.
"Leo," she whispered. "She's infected."
Leonardo raised his gun, but Selene smiled sadly. "You can't kill what's already dying."
She pressed her hand to her chest — and light erupted, consuming the chamber.
The blast threw them backward. When the smoke cleared, the chamber was empty. Only one line flickered across the console.