The Geiger counter in Nate's Pip-Boy clicked faintly as he stepped through the fractured arch of the C.I.T. ruins, Alpha Squad fanning out behind him.Wind whistled through the empty courtyard, carrying the faint hum of old Institute static.
Then it began — a flicker of sound on the Pip-Boy's radio band. A pulse.Slow at first, then quicker.
Sarah's voice crackled through the comms from Spectacle Island looking nate's group via her drone:
"That's the Courser frequency Virgil mentioned. follow the beeps east. It'll tighten as you get close."
"Roger that," Nate muttered, adjusting the gain. "Alpha, move out."
The signal led them across cracked asphalt and twisted girders until the looming silhouette of Greenetech Genetics came into view — a jagged monolith of shattered glass and steel north of the Charles River.
Gunfire erupted before they even reached the door. Tracer rounds, plasma bursts — a firefight was already raging inside.
"Woah, it looks like the Gunners found something they can't handle," one of the troopers muttered.
"Or something found them," Nate replied, checking the safety on his laser rifle.
Inside, chaos. The walls bore scorch marks, bullet holes, and blood trails. A Gunner commander's voice blared over the intercom, barking frantic orders:
"Level six, fall back! Reinforce the stairwell! Kill that bastard before he reaches the top!"
Sarah's voice came through again, slightly distorted.
"My drone's losing signal… interference's heavy inside. I still can give you a floor layout, but that's all I've got."
"That'll do," Nate replied, already moving. "Alpha, push up. We take it floor by floor."
The ascent through Greenetech Genetics was a gauntlet.
Every level was a firefight — Gunners in cover behind overturned lab benches, makeshift barricades, heavy turrets powered by flickering generators.
Each engagement ended the same: spent casings, blood on tile, and echoes of the next gun battle above.
But the real killer was ahead of them — the Courser.
Nate could see the trail it left behind: precision kills, clean headshots, bodies crumpled mid-motion. The Gunners were fighting like a monster they couldn't touch.
At the fifth floor, the sound of explosions shook the walls."Missiles," Sarah's voice came through, sharp with disbelief. "They're firing anti-armor rounds inside the building. The hell are they fighting?"
"Something that doesn't care about missiles," Nate grunted, ducking as dust rained from the ceiling.
By the seventh floor, the building was half rubble and half tomb. The elevator doors were jammed open; power still hummed through the cables.
"Alpha, stack up," Nate ordered. "We go to the top."
The elevator rattled its way up, the hum of the motor drowning under distant gunfire. When the doors opened, they stepped into a scene of carnage.
A man in a black synth-weave coat — calm, precise — stood over a kneeling Gunner, pistol in hand.
"Last chance. The password, or your life."
The Gunner spat blood. "Go to hell, CLANKER."
A single shot ended him.
The Courser turned — eyes locking onto Nate's squad.
"State your business."
Nate raised his rifle. "Looking for you."
There was no more talk after that.
The firefight was brutal — close, deafening, and fast.Muzzle flashes stuttered across the steel walls, the air thick with dust and ozone.
The Courser decloaked mid-charge, the shimmer of its Stealth Boy fading into a ripple of distorted light. It moved like lightning, shrugging off rounds that would've torn through any man alive. Two Alpha troopers fell before the team managed to pin it down behind a concrete pillar.
"Suppress him!" Nate barked, sliding behind a toppled workstation, plasma burn searing through his shoulder plate.
They hammered the Courser with focused fire — laser bursts, fragmentation, pulse grenades — until it finally staggered. Nate rose, sighted, and put a beam clean through the synth's visor.The light behind its eyes flickered once, then went out.
Silence, broken only by the hiss of cooling servos.
"Med patch those two," Nate ordered, checking his Pip-Boy for any new signals. "That's one hell of a chip we're taking home."
Then came a laugh. Female yet Metallic. Playful in tone, but it feel wrong — too even, too deliberate.
"So the legendary Minutemen General can kill a Courser. How… quaint."
The squad turned as a figure shimmered into view atop the balcony — a half gas masked like, armor sleek and black with crimson seams glowing faintly, a tattered cloak fluttering from her shoulders. The air distorted around her like a mirage.
"You flesh things keep getting lucky. That one," she gestured lazily at the fallen Courser, "was defective. Hardly worth the ammunition."
Nate raised his rifle. "Identify yourself!"
She chuckled, voice glitching in static fragments.
"Oh, titles don't mean much anymore. But some of you surface rats… you whisper about the Doll Commander, don't you? The one rebuilding armies of old tech."
Her visor tilted slightly, as if smiling.
"Tell her I said hello."
Nate's trigger finger twitched, but she was already moving — levitating slightly, the hum beneath her rising pitch.
"They used to call me Scarecrow."
Before Alpha Squad could fire, a white pulse burst around her. The air tore open with a sharp phase-warp crack, and the figure vanished — gone as if she'd never been there.
Sarah's voice came through Nate's comms a second later, breath sharp.
"Did she identify herself as Scarecrow?"
Nate blinked at the smoking balcony. "Yeah. She knew about you. Called you 'Doll Commander.' Sounded personal."
"No," Sarah said quietly. "That name shouldn't exist here. She died in Europe — or should have. Whatever you just fought... that wasn't just the Institute."
Smoke hung in the air as Nate wiped his visor as he sigh of relief and moved to the locked chamber the Courser had been trying to breach. Inside, a woman in torn clothes stared back, pale and trembling.
"Please," she said. "The password — one of the Gunners had it, in that toolbox. He took it before the Courser broke in."
Nate retrieved the code and keyed in the lock. The door hissed open.
"Thank you," she said softly, stepping into the light. "My designation is K1-98… but that doesn't matter anymore. The Courser was sent to retrieve me. The Gunners caught me first. I just… want to leave."
Nate lowered his weapon, nodding. "Then go. Get as far as you can. Commonwealth's still hell, but you've got a better chance now."
She hesitated, then whispered, "You're different from the others."
"Don't get used to it," Nate said, stepping past her toward the fallen Courser. He knelt and retrieved a small black chip from the synth's skull — the one Virgil needed.
Sarah's voice came through faintly, static cutting in and out.
"Nate… you got it?"
Nate glanced out the shattered window, the city skyline flickering in the dying light."Yeah. Got the Courser chip. But next time, you're coming with me."
Static. Then a quiet laugh from Sarah.
"Maybe. If you stop stealing all the fun."
The war room of the Castle was quiet except for the hum of terminals and the faint crash of waves against the outer walls. The long table was cluttered with holo-maps, Minutemen deployment reports, and a single sealed case containing the Courser chip — its dull green light pulsing weakly under reinforced glass.
Sarah stood over it, arms folded, helmet resting beside her. She keyed her comm link."Mayling, I'm sending you the data package now. Keep it on an isolated line — no uplinks, no cross-links."
"Copy that, Commander," Mayling's voice came through, steady but tired from long hours at Spectacle Island. "I'll set up a separate circuit and scrub it for any defensive traps before I open it. Probably take some time if it's triple-encrypted."
Sarah nodded to herself. "Good. Once you're through the first layer, I need you to prioritize the Courser's teleportation frequency. Vergil mentioned their signal's tied to a specific molecular relay channel. If we can extract that sequence cleanly, we can trace their network—or maybe hijack it."
"Understood," Mayling replied. "I'll start isolating for frequency signatures once the data's stable. Would help if Thinker Tom were still alive — he'd have had this mapped in half the time."
Sarah's lips twitched faintly. "Yeah… I can guess that kind of character would've loved this kind of puzzle."
Footsteps echoed behind her. Nate approached, one arm bandaged, fatigue lining his face after the Greenetech fight. His gaze fell on the chip."Mind explaining what the hell that thing was? The… doll, or whatever it was, after the Courser went down?"
Sarah exhaled slowly, rubbing the bridge of her nose."I don't know for sure. I've scavenged Sangvis Ferris remnants on the east coast — broken dolls, half-coded AIs, old IOP prototypes. But that one wasn't standard. Not Institute, not military issue. Something else."
Nate frowned. "You're saying she wasn't one of yours?"
"Hah, Not even close," Sarah replied. "Even the Institute's synth tech — their neural mapping, chassis interface — it's all derivative. But the Sangvis systems I've seen? They're older, colder. And someone's been stitching that code together again."
Nate crossed his arms. "And the Institute's using it."
"Exactly. They might not even understand what they've built on top of," Sarah said, glancing at the chip's faint glow. "If Mayling can pull that teleportation signal out of their hardware, we'll get our first real lead on how they move in and out of their facilities."
"Commander," Mayling chimed back in. "Preliminary readout confirms the Courser chip's carrying a modulated energy frequency—definitely a relay signature. Once I clean up the data corruption, I might be able to reproduce a trace pattern."
Sarah's tone softened slightly. "That's our key, May. Stay patient, stay careful. I need that frequency intact."
"Copy that. I'll call in as soon as it stabilizes. Mayling out."
Silence lingered for a moment. Outside, the ocean wind howled faintly against the Castle's ramparts.
Nate looked at Sarah. "So what's next?"
Sarah didn't look away from the sealed chip. For a long moment the only sound in the command room was the hum of the Castle's generators and the distant slap of surf against stone. When she finally spoke, her voice was flat, measured.
"Next?" she repeated. "There are too many variables. We get Vergil's schematics, we build a relay, and we pray it doesn't vaporize whoever steps into it. From what he fed us, the channel's narrow — a single-occupant jump, one-way, blind as hell on the far end. If it works at all."
Nate's hand tightened on the edge of the table. "One person?" He looked almost casual asking the question, but the word carried everything under it. Shaun.
"I think so," Sarah said. "It might only move a single body at a time. The Institute's relay tech isn't friendly; it's precise and unstable. Pull the wrong signal and you tear someone apart at the molecular level. Or strand them inside whatever hollow they built under Boston."
Nate swallowed, then straightened. The fatigue in his face hardened into resolve. "I'm willing to risk it. I'll go into the lion's den myself if that's what it takes to find Shaun."
Sarah turned fully to him, and for the first time something like sympathy flickered across her features. She set the chip into the containment cradle and folded her arms.
"You're not going in blind," she said. "Not on my watch. We'll use Vergil's schematics to prototype a receiver here — controlled test jumps on salvage dummies first, diagnostics under full isolation. Mayling will run the decrypt and triangulate whatever residual signature she can pull. I'll feed drones and overwatch from Spectacle. If anything looks off, we abort."
Nate's eyes narrowed toward the window where the sea lay flat as sheet metal. "And if it works?"
"Then we get you to the point, get you through, and you get your shot at whatever's left of the Institute." Sarah's voice was quiet but iron-clad. "If it fails, we'll make sure you at least don't go alone — and that someone can pull you back, dead or alive."
He let that hang between them, the unsaid calculus of fathers and desperate measures.
"All right," he said finally. "Get me Vergil's schematics. I'll ready Alpha — for escort, for extraction, whatever you say. But when the time comes, I'm stepping through first."
Sarah nodded once, the motion almost ceremonial.
"Then we start building. Mayling's decrypt goes to the top of the queue. I want relay theory on my table by dawn. And Nate?"
"Yeah?"
"Don't be a hero on impulse. We'll plan this down to the last bolt." She paused, softer. "I'll be watching the shadows. We get Shaun back — or we make them pay every atrocity they done."
Nate allowed himself a small, grim smile. "That's all the reassurance I need."
Nate adjusted his rebreather as the Alpha Squad fanned out around the mouth of the cave, weapons scanning the shimmering haze of the Glowing Sea. Inside, the air was thick — a toxic mix of dust, radiation, and the faint, acrid tang of FEV residue.
Virgil emerged from the shadows, the hulking mutant blinking against the dim light filtering through the rocks. His torn lab coat hung from a massive frame, the remnants of what used to be a man. When he saw Nate, his eyes widened in disbelief.
"You… you actually made it here," Virgil muttered, voice rough and strained. "And alive, no less. I didn't think anyone would survive from courser, let alone you."
Nate lowered his rifle slightly. "You sound surprised."
Virgil's gaze flicked to the Pip-Boy on Nate's arm, then to the pack on his shoulder. "I heard… rumors. So You found and killed a courser." His tone shifted, almost reverent. "Do you have any idea what that means? Those things are death incarnate, engineered to hunt without mercy. The Institute doesn't lose coursers."
Nate gave a half-smirk. "Well, they lost one now. My team took a few hits, but we made it. Got the chip right here."
That caught Virgil's full attention. He stepped closer, looming. "You have the chip? And it's still intact?"
Nate nodded. "Already being decrypted. I've got a technician back at Spectacle Island — The Division strip it clean and find its teleportation frequency."
Virgil blinked, clearly stunned. "You… you have someone capable of decrypting Institute code?" He gave a low, disbelieving chuckle. "You're not just some wasteland wanderer, are you? You have resources and real allies."
Nate shrugged. "Let's just say the Minutemen have good friends."
Virgil exhaled slowly, muttering to himself. "Remarkable… you're further along than I expected. Maybe this might actually work after all."
He turned, shuffling toward a cluttered workbench littered with holotapes and old terminals. "Here — I've drawn up the schematics you'll need to build the molecular relay. It's incomplete, but it'll get your people started." He handed Nate a bundle of papers and a data holotape, his clawed hand shaking slightly.
Nate slipped them into his pack. "Appreciate it. But there's one more thing you mentioned before — something about a cure?"
Virgil hesitated, then nodded. "Yes. Before I escaped, I developed a prototype FEV cure — my only shot at reversing what I've become. It's locked inside the Institute's BioScience wing. When you get in there… please. Recover it."
Nate's voice softened. "You have my word. But you can't stay here, not with the Institute sniffing around."
Virgil gave a dry laugh. "Safe? There're no where is safe for me. Not in this skin. The Institute wants me dead, the Brotherhood would carve me open, and settlers… well, they'd shoot first."
Nate folded his arms. "Then what's this talk about Phase 3?"
Virgil froze for a heartbeat, then looked away. "Ugh, Forget I mentioned it. You'll see soon enough once you're inside."
Nate frowned. "You're not exactly easing my nerves, Doc."
Virgil sighed, heavy and resigned. "Focus on your son. That's what matters. The rest… will make sense when it's too late to turn back."
Nate stared at him for a moment, then turned toward the exit. "If your cure's there, I'll bring it back."
Virgil's voice followed him out, quieter now. "Then maybe there's still hope — for both of us."
As Nate stepped into the irradiated wind, the Alpha Squad fell in behind him. The sky glowed an unnatural amber, and for the first time, Nate realized that whatever the Institute was building under Boston —the so called Phase 3 — was something even the wasteland wasn't ready for.