The world reassembled around Nate with a bone-deep hum — light, pressure, and static tearing apart and fusing again until the air settled cold and sterile.
The Institute.
White walls. Fluorescent lights. The sharp tang of ozone. It was too clean — too perfect — and that made his skin crawl.
A calm voice spoke through the hidden speakers:
"Welcome. Please proceed to the elevator ahead. We've been expecting you."
He moved cautiously. The door sealed shut behind him with a hiss, locking him in. Nate exhaled, spotting a terminal near the relay platform — his instincts as a soldier kicking in.
Sturges' holotape.He pulled the small chip from his pouch, recalling the mechanic's words: "Plug it in once you're inside, big guy. It'll grab whatever we can from their system."
Nate frowned. That's usually Sarah's department… But it didn't matter. He needed intel. He needed leverage.
He inserted the holotape. The screen came alive with code. The scan only lasted seconds before a message blinked:
[SCAN COMPLETE – DATA EXTRACTED]Holotape Ejected.
Nate pocketed it, stepped into the elevator, and muttered,
"Alright, let's see what kind of hell you've built down here."
The elevator hummed as it rose through gleaming white corridors. The voice guided him again, soft but clinical:
"You are safe here. Please, continue forward."
Nate's jaw clenched. Safe? Not a single soul in sight, yet the walls seemed alive — humming, whispering, watching. The deeper he went, the more wrong it felt.
At last, the elevator opened to a small chamber — toys scattered on the floor, a cot, and a small boy standing there, staring with wide, frightened eyes.
"Who… who are you?" the boy asked, voice trembling.
Nate froze. His heart leapt into his throat.
"Shaun? Is that really you?"
He took a step forward — but before he could reach the boy, a door opened behind him.
"That's close enough," said a calm, aged voice.
Nate turned. The man in the lab coat looked at him with a detached curiosity — the posture of someone who hadn't seen sunlight in decades.
The man murmured something — a code phrase.
"Shaun....S9-23 Recall code: Cirrus."
The boy went still, eyes vacant, his voice cutting off mid-breath.
The man didn't flinch. His voice was calm — too calm.
Man:"He's not your son… not exactly. He's a synthetic — a model. I wanted you to meet him first. To understand."
For a heartbeat, Nate just stared. The words hit harder than any bullet. His voice cracked as anger flooded in.
Nate:"You… what? You built a copy? You took my son and made a toy out of him?!"
His grip tightened on the rifle.
Nate (roaring):"I'll make this simple — WHERE IS MY SON?!"
The older man took a slow step forward, hands open, unarmed.
Man:"Please. Lower your weapon. There's no need for this. He's here… in the Institute. Closer than you think."
Nate's breath hitched. The room felt like it was closing in. His gaze flicked between the stranger's lined face, the white hair, the faint echo of something familiar behind those calm eyes.
And then the man said it — softly, almost with pity.
Man:"I'm… your son, Nate. I'm Shaun."
The words didn't make sense. They couldn't. Nate blinked, the rifle trembling slightly.
Nate (staggering back):"No… no, that's not… Shaun was a baby. I— I saw him taken. He was ten when I thought—"
Shaun (gently):"You believe it's been ten years since the Vault opened. That you've been searching for a child. But that's not how long it's been."
He stepped closer, voice steady, patient.
Shaun:"When you were in cryogenic stasis, you had no sense of time. You were released… long after the world forgot. Not ten years — sixty. The boy you remember is long grown."
Nate's mouth went dry. He stared at the man — his son — and for the first time since the bombs fell, he had no words.
Shaun (quietly):"I was raised here. By the Institute. And now… I lead it."
He held Nate's gaze, a faint sorrow flickering behind the calm.
Shaun:"I know it's hard to accept. But the child you lost… the man you see now… are one and the same."
His breath came shallow, hands trembling around the rifle he no longer remembered raising.
Sixty years.Shaun.The Institute.
It all bled together like a nightmare he couldn't wake from.
He staggered back a step, voice breaking.
Nate:"You're telling me… all this time, all the searching — all the people I fought, the blood I spilled — my son's been down here?"
Shaun didn't answer right away. His expression was unreadable — not cruel, not kind, just measured.
Shaun:"In the year 2227, our research reached a limit. Synthetic evolution — Gen 2, Gen 3 — but the barrier of imperfection remained. We could mimic life, but not recreate it. We needed a pure genetic baseline. Something uncontaminated by radiation or mutation."
He turned slightly, looking toward one of the glass-paneled walls where a soft hum resonated from deep below.
Shaun:"That's when the Institute found Vault 111. And you — and me."
Nate's throat tightened. The truth clawed through every memory he'd buried since Concord.
Nate (hoarse, barely holding it together):"That's why they took you? My son — for a goddamn experiment?"
Shaun's eyes flicked back to him, calm as a surgeon.
Shaun:"In a manner of speaking, yes. I was the logical starting point. Untainted human DNA. My genome was… the foundation of our success."
Nate's grip on the rifle loosened, the barrel lowering as his strength drained out of him.
Nate:"You were their specimen…"
Shaun tilted his head slightly — not defensive, not ashamed.
Shaun:"I was their key. The bridge between what humanity was — and what it could become."
Nate's face twisted in disbelief, fury warring with heartbreak.
Nate (voice rising):"You call that progress? You call stealing a child — my child — evolution?"
Shaun didn't flinch.
Shaun:"The surface is chaos, Father. You've seen it. The Institute doesn't destroy — it rebuilds. Refines. Down here, humanity endures. Because of me… and because of you."
That last phrase hit him like a blade. Nate took a long, unsteady breath, eyes glistening.
When the conversation ended, Shaun clasped his hands behind his back again and turned toward the upper walkway that led deeper into the Institute's administrative sector.
"I believe that's enough for one day," he said evenly. "You've seen the Institute for what it is — not myth, but reality. For now, I'll allow you to explore freely. We have nothing to hide from you."
Nate crossed his arms, skeptical.
"That so? You've been watching the surface for years, snatching people, replacing them with synths — and now you wanna play the gracious host?"
Shaun only smiled faintly.
"Perspective, Father. You call it kidnapping. We call it preservation of potential. But if it puts your mind at ease…"
He gestured to a nearby synth, its smooth white chassis gleaming under the sterile lights.
"You won't be alone. I've assigned someone familiar to you."
From the far end of the corridor, footsteps approached — light, precise, carrying a rhythm that didn't belong to any human soldier.
When the figure emerged from the glass partition, Nate's breath caught.
She wore the Institute's field-gray uniform variant — armored weave beneath the coat, weapon holstered tight against her thigh. Her long hair, once pale silver, was now dyed jet black; an eyepatch covered the right side of her face where circuitry had once glowed faintly beneath synthetic skin.
But even with all the cosmetic changes, Nate knew her.
"...M16A1?" he muttered, disbelief hardening into anger. "What the hell is she doing here?"
Shaun paused by the railing, tone unbothered — clinical, almost proud.
"Ah. So you do recognize her. Or rather, the body that once carried that designation. She's been reconditioned — recovered from the field after that rather… chaotic event in your Commonwealth. A remarkable piece of engineering, that one. Her neural map was fragmented, but salvageable."
The woman's remaining eye glowed faintly green as she approached. Her voice, calm and clipped, carried none of the warmth Nate remembered from Sarah's unit.
"Director Shaun assigned me to ensure your safety within Institute grounds," she said. "You may refer to me as Beluga."
Nate blinked. "Beluga? That some kind of joke?"
"Negative. It's my designation."
He turned toward Shaun, voice low with rising fury.
"You reprogrammed her? After everything she did to help me? She nearly died stopping Kellog!"
Shaun's expression didn't waver.
"We restored her. The memory patterns from her previous… service were corrupted beyond functional parameters. She is stable now — loyal, efficient, and far more useful under proper supervision. In fact," he added with a faint smile, "you should be grateful. She knows your behavioral patterns quite well. A perfect escort."
Beluga's eye flicked between the two men, unblinking.
"Director, shall I begin the orientation protocol?"
"Yes," Shaun said, already turning away. "And please ensure our guest doesn't wander anywhere… sensitive."
As Shaun's footsteps faded into the white corridors, the hum of the Institute's systems returned — a mechanical heartbeat pulsing through the floor.
Nate and Beluga stood in silence for a long moment.
He studied her — the small scars under the eyepatch, the polished metal at her wrist, the faint whine of servos under her skin. She looked the same, but there was nothing old trace of her essence left in her stance.
"You really don't remember me, do you?" he said quietly.
Beluga tilted her head, her expression unreadable.
"Memory integrity prior to Institute recovery is classified as non-recoverable. If you wish to proceed with your exploration, I will accompany you."
Nate let out a slow breath, his frustration cooling into something more hollow.
"Yeah. Sure. Lead the way, Beluga."
As they walked through the shining halls — synths passing in orderly silence, white lights reflecting off the polished floor — Nate couldn't shake the feeling that the woman walking beside him wasn't just an escort.
Using her as a warning.
The hum of the Institute grew softer as Nate followed Beluga into the Bioscience Division. The air here was warm, moist — alive in a way the sterile white halls weren't. Rows of bioluminescent plants lined glass-walled corridors, their roots fed by thin trickles of nutrient-rich water that pulsed in rhythm with the pumps beneath the floor.
Children in lab coats scurried quietly between greenhouses, carrying tablets and sample trays. The smell of earth — real, unfiltered soil — filled the air. It reminded Nate of the Vault hydroponics labs, of the days before the world above burned.
"This place… it's like a damn paradise," Nate muttered under his breath."Efficient use of resources," Beluga replied tonelessly beside him.
He spotted two men near a workstation. One — a tall, silver-haired scientist — was adjusting a console that displayed rows of genetic markers. Clayton Holdren, the bioscience division head, if Nate remembered right from the wall plaque. The other, a younger man named Karlin, was studying a tank where a translucent creature floated — half amphibian, half something else.
Holdren turned when he saw Nate, offering a polite, clinical smile.
"Ah, the surface visitor. I was told you'd be observing. I trust the Director has made you comfortable?"
"Depends how you define comfortable," Nate said, glancing at the biotanks. "You folks sure know how to grow a salad."
Holdren chuckled softly.
"We grow far more than food here, Mr. — Nate, wasn't it? This bioscience division sustains the Institute. Our work ensures survival beyond the rot of the surface. Purified water, synthetic protein, advanced medicine… even the gorillas in the atrium are fully engineered constructs."
Nate raised a brow. "Gorillas?"
Karlin looked up, proud.
"Two of them. Perfectly functional, even simulate aggression responses. Proof that we can recreate any species — given enough data and DNA integrity."
Nate tried to keep his face neutral, but a thought gnawed at him. All this brilliance… and they still made monsters like the super mutants.
As he moved through the lab, his eyes caught a narrow hallway branching east — dimmer, older, the walls less polished. A small sign read: "RESTRICTED ACCESS – LEVEL 3 CLEARANCE." The lock plate flickered weakly.
Beluga followed silently, her bootsteps echoing behind him.
"You not gonna stop me?" Nate asked, glancing back.
Beluga didn't respond immediately. Her uncovered eye dimmed slightly — a flicker of something like static shimmered in her iris. Then she closed it, face turning away for just a heartbeat too long.
"...…"
The silence told Nate everything he needed to know.The Institute hadn't finished reprogramming her. Somewhere in that machine-precise mind, pieces of the old M16A1 still resisted.
He crouched by the panel, overriding the novice lock easily with his Pip-Boy. The door hissed open. A wave of stale, cold air spilled out — thick with the metallic tang of disinfectant and old decay.
The FEV Lab was nothing like the rest of the Institute.The clean white walls gave way to stained metal and dark glass. The hum of life-support systems was replaced by the low, sickly drone of dormant machines. Rows of containment tanks stood shattered or sealed with corrosion, faint green residue clinging to their interiors.
Nate stepped closer to one of the terminals — the logo on the screen read Forced Evolutionary Virus – Project Documentation. He scrolled through fragmented logs: entries dated decades ago, notes signed by Institute geneticists long dead or missing.
"Subject degradation exceeds expectations. Results unsalvageable. Transfer operations to surface-level test sites. Requesting additional human specimens from Retrieval Division."
Nate's jaw tightened. So Virgil was right.
This was where they made the monsters that haunted the Commonwealth — where science and arrogance mixed into something too toxic to contain.
He turned toward Beluga, who stood just outside the doorway, unmoving.
"Do you knew about this?"
Her expression didn't change.
"This section is decommissioned. Not part of current operational parameters."
"Bullshit. You people dumped this poison into the world. You guys made them."
Her gaze lingered on the cracked glass tank beside him.
"Data incomplete," she said, but her tone had shifted — softer, uncertain. "However… evidence suggests Institute responsibility. Term 'containment failure' appears frequently in surviving logs."
Nate ran a hand through his hair, exhaling hard. "Yeah, figures."
He turned toward the back wall where a half-collapsed chamber stood — the remains of an old teleportation relay. The stabilizer coils were burned out, the flooring warped by energy discharge.
He knelt beside the terminal there and wiped off the dust. The logs showed only a few surviving lines, but one stood out:
'Subject V. authorization override. Relay coordinates scrambled — external activation successful. Escape confirmed.'
Virgil's signature.
"So this is where he did it," Nate murmured. "Where he escaped."
Beluga's voice came quiet behind him, almost like an echo.
"You admire him."
"He had guts. He saw the truth and walked away."
"And you?"
Nate stood, meeting her gaze. "I came to end it."
The silence that followed was deep — broken only by the hum of dead machines remembering what they once were.
Beluga's fingers flexed at her side, faint servo motors whining. For the briefest moment, she looked away — as though something in her own memory stirred, and she didn't know how to process it.
Nate turned off the terminal and grab the FEV cure then place into his pocket and stepped past her.
"Come on. I've seen enough."
As they walked back into the bright corridors of Bioscience, the smell of soil and green life returned — but to Nate, it all felt hollow now.
The Synth Retention Bureau was colder than the rest of the Institute — not in temperature, but in atmosphere.The lighting dimmed to a sterile white-blue glow, the hum of terminals louder here, sharper, almost surgical.Every motion, every conversation felt observed.
Beluga kept a step behind Nate as they entered.Rows of glass cells lined the walls, each holding storage pods, scanning devices, and half-assembled synth units suspended in diagnostic fields.Nate couldn't help but feel he'd walked into a police station fused with a morgue.
A man in a sharp white coat, posture rigid, turned from his terminal as Nate approached.His voice was precise, clipped, and controlled — the kind of tone only bureaucrats or interrogators used.
Justin Ayo: "Ah, you must be the visitor from the surface. The one who neutralized a Courser. Impressive, I must say. Not many outside the Institute can claim that."
Nate: "Guess he picked the wrong day to come after me."
Ayo gave a thin, amused smile and folded his arms.
Justin Ayo: "Tell me, then — how did you do it? Our Coursers are built for surgical precision and overwhelming force. I assume you didn't manage that alone."
Nate studied him, trying to read the man's real intent behind the curiosity.
Nate: "Minutemen training under my command. I've got military experience — enough to make do when things go south. We had the numbers, and the strategy. That's all."
Ayo hummed, unconvinced, tapping his chin thoughtfully.
Justin Ayo: "Numbers. Strategy. Discipline. Yes… those are things most of the surface rabble lack."
He turned back to his console, pulling up a holographic record of synth retrieval operations.
"You know, Director Shaun has a habit of romanticizing the Commonwealth — thinking there's some spark of order left in the ruins. But I find reality tends to prove… less flattering."
Nate's jaw tightened.
Nate: "Maybe that's because you people keep snatching anyone who shows potential. You build replacements instead of trusting the real thing."
Ayo chuckled quietly, eyes still on his display.
Justin Ayo: "You call them 'replacements.' We call them corrections. You've seen the world above — chaos, violence, regression. We, on the other hand, are trying to restore stability through design. To engineer reliability."
He turned back, expression cool and composed.
"Besides, it's not as if your kind hasn't benefited. That Courser you destroyed carried data crucial to our new containment systems. You've given us a challenge to improve upon."
Nate: "You sound proud of that."
Justin Ayo: "Shouldn't I be? Progress demands conflict. Without resistance, innovation stagnates."
For a moment, Ayo's tone slipped — not arrogance, but fatigue.
"Still… I will have no end of mockery from the ringleaders after this. Losing a Courser to a Vault Dweller? Unthinkable. Especially when Dr. Zimmer left us to clean up the Bureau alone."
He sighed, pinching the bridge of his nose.
Nate: "Zimmer? That name's been floating around. He your boss?"
Justin Ayo: "Technically, yes. I'm merely filling the position of SRB Director in his absence. He's overseeing a 'high-priority retrieval' elsewhere."
Ayo's voice faltered slightly on the word elsewhere, and he adjusted his glasses before continuing, tone regaining its smooth precision.
"Still, the Bureau functions as intended. Our work never stops."
Nate's eyes narrowed — the small tells didn't escape him. Zimmer wasn't "overseeing" anything. He was missing.But Ayo's tone made it clear that topic wasn't open for discussion.
Beluga, silent beside him, seemed to note it too; her good eye flickered faintly with amber light, recording every detail.
Nate: "You ever think maybe your 'retrievals' are the reason people up top fear you?"
Ayo smirked faintly.
Justin Ayo: "Fear is merely an evolutionary response to misunderstanding. In time, they'll learn what we truly offer."
He turned back toward his console.
"You've seen enough for today, I think. The Director wanted you to explore, not to argue ethics. please leave."
The sterile brightness of the Robotics Division hit Nate the moment the doors slid open. The air smelled faintly of heated metal and sterilized plastic, humming with the sound of machinery too precise to belong to any living thing.
From the balcony, he could see everything — the heart of the Institute's creation engine. A vast chamber stretched below, dominated by a red-glowing pool at its center. Mechanical arms dipped into it in perfect rhythm, pulling out limp, pale forms that gradually took on the appearance of humans.
Synths. Freshly born. Naked, blank-eyed, and silent.
One by one, they climbed out of the viscous pool, guided by drones into a sealed corridor that led deeper into the facility. None spoke. None resisted.
It was… unsettling.
A man in a lab coat stepped beside Nate, his voice calm, reverent even.
Alan Binet: "You're witnessing the birth of the future, General. Third-generation synths — indistinguishable from us, yet stronger, faster, tireless. Humanity perfected."
Nate's expression didn't change. He gave a polite nod, keeping his voice neutral.
Nate: "Impressive work you've done here."
Alan Binet: "Work? This is art. Each of them is a triumph of human engineering. No more hunger. No more disease. No more chaos of emotion."
Nate let the man talk. He'd learned something from walking through the last two divisions — Bioscience's politeness, Synth Retention's arrogance — every section here had its own justification for control. Everyone believed they were saving the world.
He wasn't about to argue. Not yet.
Instead, he rested his hand on the railing and watched another synth rise from the red liquid, its features unformed, its eyes flickering with confused motion before being led away.He didn't say what he was thinking — that it looked more like a factory for people than a sanctuary for science.
Alan Binet: "I can see you're overwhelmed. It's a lot to take in."
Nate: "Yeah. You could say that."
Binet smiled faintly, mistaking Nate's silence for awe.
Alan Binet: "Once you understand the purpose behind it all, you'll see — we're not replacing humanity, we're preserving it in a better form."
Nate gave a small nod, hiding the chill that ran through him.He'd already seen enough to know this place wasn't a haven of progress — it was a cage built from good intentions and cold logic.
Behind him, Beluga watched quietly. The red light reflected across her face, and for just a moment, Nate thought he saw something human flicker in her one good eye — uncertainty.
He didn't speak of it.He simply turned away from the red pool, his silence saying more than any argument could.
The doors to Advanced Systems slid open with a hiss of sterilized air, revealing a room alive with blue light and static hum. Here, science wasn't quiet — it crackled. Coils arced faintly with electricity, plasma casters hummed on test benches, and holographic schematics rotated in midair above the researchers' stations.
Nate could feel the temperature shift, that subtle static charge before a thunderstorm. He'd seen energy weapons before, but nothing this refined. Nothing this… alive.
A woman turned from a console, dark hair streaked with grey and tired eyes that had seen too many failed experiments. She didn't bother hiding her exhaustion.
Dr. Madison Li: "You must be the surface dweller everyone's talking about. The Director's father, right?"
Nate gave a nod. "That's what they tell me."
She studied him for a moment, then returned to her terminal. "I'm Dr. Li. You'll find this division… a bit different from the others. We work on things that actually keep this place from falling apart — plasma research, teleportation physics, the reactor. Things that matter."
Nate's gaze swept the lab — the firing range where a young synthetic Shaun stood beside a researcher, firing a miniature plasma pistol under careful supervision. For a moment, Nate froze. The boy's stance, the way he squinted, reminded him painfully of a memory he hadn't thought about in years.
Dr. Li: "Don't look too shocked. The Director thought it would be comforting to give the younger staff something to look after."
Nate exhaled through his nose, forcing down the ache in his chest. "Yeah. Real comforting."
She changed the subject quickly, gesturing toward the heavy machinery at the room's far end. "Your visit isn't just for sightseeing. The Director gave orders — you're being granted relay access."
Nate: "Meaning?"
Dr. Li: "Meaning, I'm installing a custom sub-frequency link to your Pip-Boy. You'll be able to teleport between the surface and the Institute without needing our signal interceptors. It's a one-way secure relay. Don't lose that thing — or you'll be walking home through a few hundred meters of solid rock."
Nate raised an eyebrow. "Appreciate the confidence."
Dr. Li gave a humorless smile. "Confidence is the only thing keeping this place running."
As she finished linking the relay, Nate noticed a sealed corridor across the lab — shimmering behind a forcefield. It pulsed faintly with red light. He couldn't see beyond it, but something about the energy readings made his Pip-Boy flicker for a moment.
Nate: "What's behind that field?"
Dr. Li didn't even look up. "Classified. Even I don't have clearance. Don't ask again."
Her tone ended the matter. Nate didn't press it — though the faint hum of that field stayed with him.
Minutes later, the relay connection synced with his Pip-Boy. Li shut down her console.
Dr. Li: "Done. You can come and go now. Just… remember where you are. The Institute's patience is thin, even for the Director's father."
Nate: "Wouldn't dream of wearing out my welcome."
Leaving the lab, Nate passed the young synth Shaun again — the boy looked up from his plasma pistol and smiled faintly. Nate forced a smile back before the elevator doors closed.
At the upper level, Beluga stood silently by the Director's chamber entrance, her posture perfect, her one eye glowing faintly under the sterile light. Nate slowed as he passed her.
Nate: "Guess this is where we part ways."
Beluga didn't respond — just nodded once, mechanically.
The elevator opened to the relay chamber, its air filled with faint ozone. Nate stepped onto the platform and looked around one last time. The pristine world beneath the earth, so clean it felt suffocating.
"I wish for Peace," the Director had called it.But to Nate, it felt like a cage with better lighting.
As the platform powered up, he looked down at his Pip-Boy — the relay indicator now glowing green.
Nate (quietly): "Let's see if the surface still feels like home."
Light engulfed him — and with a crack of energy, he vanished from the Institute, leaving only the echo of the teleportation hum behind.