Chapter 1: Shadows in the Club
Chapter Text
Clary Fray had never felt so out of place.
Pandemonium pulsed with bass so heavy it rattled her bones. Strobe lights flickered across the sweat-slick crowd, catching in clouds of smoke from the machines overhead. The air reeked of perfume, alcohol, and heat. All around her, bodies pressed close, moving in rhythm, grinding to a beat she couldn’t quite catch.
Simon had dragged her here, promising it would be fun, and maybe it was, for him. He’d vanished toward the stage within minutes, guitar picks stuffed in his jacket pocket just in case he got lucky with a band. Clary, meanwhile, hovered near the edge of the dance floor, clutching her drink like a lifeline.
She’d always been different. Quiet where Simon was loud, hesitant where he was reckless. And lately, she’d been sketching strange things she couldn’t explain, twisting marks, lines that belonged on skin, not paper. She hadn’t told her mom. She hadn’t told Simon either. The drawings felt private, like they were secrets she wasn’t meant to share.
Now, staring into the crowd, she wondered if the shapes in her sketchbook weren’t imagination at all.
A figure stood too still among the moving bodies. His eyes gleamed unnaturally bright in the flashing lights, and the shadows around him seemed thicker, bending unnaturally with every strobe. Clary blinked once, twice, telling herself it was a trick of the lights.
It wasn’t.
The man turned, and his face wasn’t human.
Her drink slipped from her hand, crashing to the floor as she stumbled back. She collided with a dancer who shoved her aside with a curse, but Clary hardly heard him. The creature’s lips pulled back into a smile that showed teeth that were too sharp. And it was walking toward her.
Her mind screamed move, run, scream, but her body locked up.
The creature lunged.
Steel sang.
The demon dissolved into black smoke inches from her, scattering like ash on the floor. Clary’s lungs seized. She tried to scream, but no sound came out. A hand clamped around her wrist, firm, pulling her upright.
“Careful, little sister.”
The voice was low, rough, carrying an edge that made her skin prickle.
She turned.
The boy holding her looked no older than she was, but there was nothing boyish in him. His hair was pale, his skin almost too white, and his eyes green, sharp, identical to her own stared at her with a familiarity that hollowed her out. His grip on her wrist was bruising, but he didn’t let go. His smile was jagged, dangerous.
Another voice cut through the music, calm where the first was sharp.
“Jonathan.”
From the shadows stepped another boy, taller, broader, older. His hair was black, his presence commanding. His blade dripped ichor as he slid it back into place. He moved like he’d fought a hundred battles, each one burned into his posture.
Clary tore her arm free, stumbling back. “Who... who are you?”
The pale one, Jonathan, smirked. “You don’t recognise us? Good. That’ll make this easier.”
The taller one’s gaze softened, though only slightly. “We’re your brothers. Jonathan. Sebastian. You weren’t supposed to find this world. Not yet.”
Her mind blanked. Brothers? She had none. She’d grown up an only child. Her mother would’ve told her, wouldn’t she?
The music stuttered, a beat skipping. The lights overhead flickered. The shadows across the ceiling spread like cracks in glass.
Sebastian swore. His blade was in his hand in an instant. “Circle.”
Figures slipped from the crowd, cloaked in black, runes glowing faintly on their skin. Ordinary clubgoers passed through them unaware, oblivious to the danger closing in.
Jonathan’s blade lit with silver fire. He shoved Clary behind him, his voice a growl. “Stay there. Don’t move.”
Clary shook her head, panic clawing at her throat. “I don’t even know you!”
“You will.”
The first Circle loyalist lunged. Sebastian’s blade met theirs, sparks flying. Jonathan was already moving, his strikes vicious, efficient. Demons slipped through the cracks of the crowd, clawing their way toward them.
From across the club, Simon’s POV: he saw Clary vanish in a storm of shadows. He blinked, rubbed his eyes, thinking it was just strobe lights. But then he saw steel glint and people fighting where no one else seemed to notice. He shouted her name, but his voice drowned under the bass.
Back in the fight: Jonathan moved like a storm, cutting through a soldier with brutal efficiency. He didn’t fight fair; he fought to kill. Sebastian’s style was colder, precise, every strike calculated. Together, they were unstoppable and terrifying.
Clary’s pulse roared in her ears. She stumbled backward, hands trembling. She wanted to run, to scream, but her blood thrummed with something sharp and hot. Her fingers itched for a pen, for ink, for the strange shapes she’d been drawing for weeks. She didn’t understand it, but she felt it.
Jonathan caught her arm as another soldier collapsed at his feet. His face was wild, fierce, his eyes blazing. “You’re not safe here. You’re not safe anywhere. Do you understand? He’ll come for you.”
Her voice cracked. “Who?”
Sebastian slammed a soldier against the wall, blade through their chest. He looked back at her, calm, voice steady even in the chaos.
“Our father.”
The word sliced through her.
Father.
Valentine.
The name rose unbidden in her mind, bitter and burning, though she didn’t know why.
Jonathan grabbed her, dragging her toward the back. Sebastian flanked her, cutting down another soldier with brutal precision. Together, they shoved her through the emergency exit, out into the pouring rain.
The city sprawled before them, blurred by stormlight. Sirens wailed in the distance.
Inside the club, Simon fought against the press of the crowd, shouting her name, but Clary was gone.
Outside, Clary’s chest heaved as her whole world fractured. She wasn’t an only child. She wasn’t safe. And somewhere out there, a father she’d never known was hunting her.
The two strangers who claimed to be her brothers were the only ones standing in his way.
And Clary Fray had no idea whether that made her safer or more doomed than ever.
Chapter 2: The Runaways
Summary:
On the rain-slick streets of New York, Clary is dragged between two strangers who call themselves her brothers, Jonathan and Sebastian. The Circle hunts them relentlessly, and Clary sees firsthand just how dangerous and powerful the siblings are. But when she instinctively creates a rune to save herself, Jonathan and Sebastian realise her powers are awakening. With nowhere safe to run, Clary is forced to face a terrifying truth: her life is no longer her own, and Valentine is coming.
Chapter Text
Rain hammered against the pavement, slicking the streets with silver.
Clary stumbled as Jonathan pulled her down an alley, her shoes slipping in the water. Sebastian brought up the rear, blade still drawn, his eyes scanning the rooftops as though danger lurked behind every shadow.
“Let go of me!” Clary yanked her arm free from Jonathan’s grip, chest heaving. “I don’t even know you! You can’t just drag me out of there like—like—”
“Like we saved your life?” Jonathan snapped, whirling on her. His eyes burned in the neon glow. “You’d be dead in that club if we hadn’t shown up.”
Clary’s heart hammered. She wanted to deny it, but the memory of the demon’s teeth flashed in her mind. She hugged herself, shivering in the rain. “This is insane. Demons? Circle? Brothers? None of this is real.”
“It’s real,” Sebastian said quietly, his voice like steel under ice. He sheathed his blade with a deliberate motion, his gaze never leaving the street beyond them. “Every word. Every shadow you saw tonight.”
Clary shook her head, backing away from both of them. “No. My mom would’ve told me. She would’ve..”
“She lied to you,” Jonathan cut in, sharp and merciless. “She kept us from you. Hid you like you were fragile, like you were hers alone.”
Clary’s breath caught. “You’re wrong. She would never”
“Think what you want.” Jonathan’s mouth twisted. “But you can’t go back now. Not after they’ve seen you.”
Sebastian finally turned toward her, his expression unreadable. “He’s right. The Circle knows who you are now. You’re a target.”
Clary blinked at him, rainwater dripping into her eyes. “Why? Why me?”
Sebastian’s silence was louder than any answer.
Jonathan’s blade was in his hand again before she could press further. “Move,” he ordered. “We’re not safe here.”
The sound came, followed by dozens of footsteps. From both ends of the alley, black-clad figures closed in, runes glowing faintly on their arms.
“Circle,” Sebastian muttered.
The fight was fast and brutal. Jonathan tore through the soldiers like fire unleashed, every strike wild and vicious. Sebastian was colder, methodical, his blade finding throats and hearts with terrifying precision. Together, they were unstoppable and frightening.
Clary pressed herself against the wall, heart in her throat. She should run. She should scream. But she couldn’t tear her eyes away.
One soldier broke past them, rushing at her with a blade raised. Clary’s breath froze.
Jonathan was there in an instant, cutting him down so close the spray of black ichor spattered her face. His hand slammed against the wall beside her head, pinning her in place. His eyes burned into hers, too wild, too sharp.
“You see now?” His voice was a low, ragged growl. “This is the world you belong to. This is who we are.”
Clary’s knees threatened to give out. “I don’t belong here.”
Sebastian finished the last soldier with a clean strike, his blade gleaming dark in the rain. He looked at her then, his expression cold but steady.
“You don’t have a choice.”
The sirens grew louder, distant but closing. Jonathan finally stepped back, dragging a sleeve across his face, ichor streaking in the downpour. He grabbed her wrist again, this time with gentler force but no less firm.
“Come on,” he said. “We keep moving. He’ll come for us.”
Clary stumbled after them, rain plastering her hair to her face. “Stop saying that! Who is he? Who are you talking about?”
Jonathan glanced back, jaw tight. “Our father.”
Clary froze mid-step. “No. No, my father..”
“Valentine,” Sebastian interrupted, his voice sharper than his blade.
The name rang through her like a death knell. She didn’t know why it felt familiar, why it burned in her chest, but it did.
“You’re lying,” she whispered.
“Are we?” Jonathan’s smile was bitter. “Then why are they hunting you?”
Clary’s throat closed. Her mother’s face flickered in her mind, Jocelyn, who had always kept her safe, who had always hidden so much.
Jonathan must have seen the hesitation in her eyes, because his own expression darkened. “She ran from him. Took you. Left us.”
Clary’s chest tightened. “That’s not true.”
“It is.” His words were acid. “Ask her. If you can find her before he does.”
Sebastian cut in before the argument could spiral, his voice hard. “Enough. Not here.”
He scanned the rooftops again, rain dripping down his face. Then he sheathed his blade and stepped closer, looming over Clary.
“You can hate us. You can call us liars. But you will listen. The Circle won’t stop. Valentine won’t stop. And if you don’t stay with us, you won’t survive the night.”
Clary stared at him, trembling, her teeth chattering in the cold.
Jonathan’s hand tightened around hers, less a grip now and more a tether. His voice, though still rough, was quieter. “We’re all you’ve got.”
The silence stretched, broken only by the rain and the echo of sirens.
And then another shadow moved. A soldier had survived, crawling from the alley, blade still in hand. He lunged straight for Clary.
This time, she screamed.
Jonathan was too far. Sebastian pivoted but wouldn’t reach in time.
Clary’s hand moved on instinct. She raised it, fingers tracing a shape she didn’t know she knew. Her nails cut lines into the damp brick of the wall, a curve, a cross, a rune.
The soldier hit an invisible wall, crashing back onto the pavement with a howl of pain. Smoke curled from his skin where the rune’s light touched him.
Clary stumbled back, staring at her own shaking hand. “What… what did I just...”
Jonathan stared at her, shock flickering across his face. Sebastian’s eyes narrowed, calculating.
“You’re waking up,” Sebastian said softly. “Finally.”
Clary shook her head violently. “No. No, that wasn’t.. I didn’t..”
Jonathan caught her shoulders, forcing her to meet his eyes. “You’re one of us. Whether you want to be or not.”
The soldier groaned on the ground. Jonathan finished him with a swift strike.
Clary flinched.
Sebastian turned away, scanning the dark street. “We need shelter. Somewhere the Circle won’t find us.”
Jonathan nodded once. His grip on Clary eased, but he didn’t let go entirely.
Clary swallowed hard, staring at the rain-slick rune still glowing faintly on the wall.
Her life had ended in that club. Whatever came next, she wasn’t ready.
But her brothers weren’t giving her a choice.
Chapter 3: First Night
Summary:
Dragged into a forgotten safehouse, Clary begins to realise how little she knows about the world her brothers live in. Tensions rise as Jonathan and Sebastian clash with Jace and Alec, and the word “protection” becomes more complicated than she ever imagined.
Chapter Text
They didn’t take her home.
Jonathan’s hand was a tether, Sebastian’s pace a command. Clary stumbled through rain-slick streets, pulled along alleys that smelled of damp brick and rusted metal. They moved like shadows who knew the map of the city better than it knew itself. Clary was just cargo in their routine.
“Where are we going?” she gasped, breath burning in her throat.
“Somewhere the Circle can’t follow,” Sebastian answered without slowing. His voice was quiet, cold.
Jonathan shot her a look over his shoulder, grip tightening around her wrist. “Don’t fall behind.”
Her shoes slapped water, her hair plastered to her face, and still she fought for sense. “You can’t just drag me like this. I don’t even know you!”
Jonathan’s jaw locked. “You will.”
They slipped into an old service tunnel, the hum of the city replaced by the groan of pipes and the hiss of unseen steam. Sebastian held a witchlight stone in his palm, its glow casting his sharp features in a pale blue light. The marks on Jonathan’s throat shimmered faintly in answer.
Clary stared at them, heart hammering. “What are those? On your skin.”
Jonathan’s mouth curled, sharp and unfriendly. “Language.”
“Tools,” Sebastian said evenly. “And the reason you’re alive.”
The door they found at the end of the tunnel looked like nothing, a rusting steel slab tagged with graffiti. Sebastian tapped a sequence against it, and wards crawled over the surface, unlocking with a sound like ice cracking.
Inside, the air was cool and still. A forgotten apothecary. Dust on shelves, herbs hanging brittle from string, the faint metallic tang of old blood somewhere beneath the floorboards. Jonathan barred the door. Sebastian dropped the witchlight on the counter, and the room softened into shadow.
Clary’s adrenaline was finally leaking away, leaving her hollow and shaking. She sank onto a stool because her knees weren’t interested in negotiation. A blanket appeared, tossed at her chest. Sebastian’s way of saying you’re weak, but not dead yet.
“What was that?” she whispered, her voice raw. “Back in the alley. I drew something, and he couldn’t reach me.”
Jonathan and Sebastian shared a look.
“A rune,” Sebastian said finally. “Instinctive. Crude. But it worked.”
“I don’t know how I did it.”
“You don’t need to know,” Jonathan muttered, cleaning ichor from his blade with rough, quick motions. “It’s in you. He made sure of it.”
“Stop saying he like I’m supposed to know who you mean!” Clary snapped, louder than she intended.
“Our father,” Sebastian said, flat and unflinching. “Valentine Morgenstern.”
The name was an axe to the skull. Clary’s mouth went dry. “No. My father was nobody. My mom told me—”
“She lies,” Jonathan spat. His eyes burned with something more dangerous than hatred—hurt. “She ran. Took you. Left us.”
“That’s not true,” Clary whispered, though her certainty wavered.
Jonathan’s laugh was low and bitter. “Ask her. If you can find her before he does.”
Sebastian cut in, calmly yet sharply. “Enough. Not tonight.”
The silence that followed was thick. Clary clutched the blanket tighter, wishing it were armour.
“I have to call her,” she said finally. “My mom. She’ll be terrified.”
Jonathan stiffened. “No.”
“You can’t stop me.”
“I can,” he said, deadly quiet.
Sebastian’s gaze flicked to her, colder but steadier. “If Valentine is listening, calling her will paint a target on you both. He’ll use her to break you.”
The words landed like stones. Clary sat back down, blinking fast, determined not to cry.
The shop creaked suddenly—a noise in the back room. Jonathan was on his feet instantly, blade raised, body angled between Clary and the sound. Sebastian touched the wall with two fingers and whispered a rune, the air tightening with power.
A rat darted out. The brothers relaxed, barely. Jonathan cleaned his blade again. Sebastian returned to his post.
Clary let out the breath she hadn’t realised she was holding. “You can’t live like this,” she said, voice trembling.
Jonathan’s smile was sharp. “We’ve lived like this our whole lives.”
She wanted to scream at him, to demand a different answer, but the knock on the door stole the chance. Precise. Two beats. A pause. Then one more.
The wards shifted, and the door opened on its own.
Two figures stepped inside, framed by the hall's light: one tall, bow in hand, face calm and profound; the other broader, with golden hair damp from the rain, a stele glowing faintly in his hand.
“Institute,” the archer said, voice steady. His eyes swept the room, calculating. They stopped on Clary, softening by a fraction. “We’re not Circle.”
Jonathan’s blade rose. “Prove it.”
The blond one smirked, lifting the stele. “I could draw a rune on your floor, but I doubt your decorator would appreciate it.”
“Jace,” the archer warned under his breath.
“Right.” Jace’s gaze lingered on Clary, curious, sharp. “We’re here for her.”
“She’s not going anywhere with you,” Jonathan snarled.
Sebastian shifted his stance, blade still at the ready, but his eyes were on Alec. “Who are you?”
“Alec Lightwood,” the archer said evenly. His bow never dipped. “The Clave has ordered her protection. Not her capture.”
Protection. The word hit Clary like a breath she hadn’t realised she was starving for.
Outside, the wards shuddered. Shadows pressed against the painted glass, smearing like oil. The Circle had found them again.
Inside, weapons gleamed, runes burned, and Clary realised she had stepped into a war she didn’t understand.
And no one was asking if she wanted to fight.
Chapter 4: Siege
Summary:
The wards fall, the Circle attacks, and the safehouse becomes a battlefield. Clary’s power explodes in ways she doesn’t understand, forcing the brothers into an uneasy alliance with the Lightwoods. Survival has only one direction now... the Institute.
Chapter Text
The first crack in the wards didn’t sound like glass breaking; it sounded like a heartbeat giving out.
Sebastian froze mid-step, his head snapping toward the door. The blue witchlight flickered against the metal hinges. Jonathan was already moving, blade drawn, body tense like a coiled wire.
Alec shifted his stance, bow drawn in one fluid motion, expression steady and unreadable. Jace twirled his stele once, a habit that looked like arrogance, but it wasn’t; he was just ready.
The wards groaned again, deeper this time, a low hum that vibrated through the floorboards. Clary flinched at the sound. It felt alive, like something ancient warning her to run.
Jonathan’s voice dropped, low and sharp. “They found us.”
“Already?” Jace asked, glancing at the windows. “You didn’t exactly make it hard to follow the trail of blood.”
Jonathan shot him a glare that could’ve melted steel. “You don’t know who you’re talking to.”
“Apparently not,” Jace said lightly. “Though your dramatic entrance at Pandemonium gave me a pretty good idea.”
“Jace,” Alec said quietly, not looking at him. “Not the time.”
The wards screamed.
The door shuddered inward. Sebastian drew his second blade, face blank and calm, the stillness before lightning strikes. “Positions.”
Jonathan stepped forward, his runes blazing faintly under the witchlight. He didn’t wait for permission; he didn’t need it. He was born for this, and everyone could feel it.
Alec moved to the window, arrow notched, shoulders squared. He didn’t waste words. Jace took the other side, stele flashing once as he traced a rune across his arm: swiftness, power, precision.
The wards cracked completely. The sound was deafening.
And then the door exploded.
Shards of metal and magic ripped through the air. Clary threw up her hands and screamed, but something inside her flared instead. The shards hit an invisible barrier, dissolving into smoke before they could touch her.
Jonathan turned, eyes wide. “You did that.”
“I didn’t mean to!”
“Then mean it next time,” he snarled, swinging back toward the fight.
The Circle poured in black uniforms, glowing runes, blades sharp as sin. The brothers met them like a storm.
Jonathan moved first, blade slicing through the first soldier’s chest. Sebastian followed, cold and silent, his strikes quick and perfect. He fought like someone who had memorised the anatomy of death. Jonathan fought like someone who enjoyed it.
Alec fired arrow after arrow, each one hitting its mark with surgical precision. Jace was fire and motion, grinning through the chaos as his blade danced.
Clary pressed against the wall, heart in her throat. The sound of clashing steel filled the air. Sparks flew. The witchlight flared brighter as if feeding off the violence.
Then a scream. Not hers. A Circle soldier stumbled toward her, face half-burned from a rune gone wrong. His eyes were wild. “You!” he shouted, pointing his blade at her. “Valentine’s daughter!”
Everything stopped.
Clary froze. The air thickened. Jonathan’s blade flashed, cutting the man down before he could take another step.
The room went eerily quiet for half a heartbeat. Then all hell broke loose again.
Jonathan’s fury was unhinged now. Every strike was fueled by rage, each swing meant to destroy, not just defend. “Don’t. Say. His. Name.”
Sebastian’s tone cut through, icy and sharp. “You’re losing focus.”
Jonathan’s blade sliced through another soldier. “I’m making a point.”
“Save it for later.”
Clary barely heard them. Her ears rang. Valentine’s daughter. The words spun around her head like a curse she didn’t understand.
Alec moved in front of her just as another soldier broke through the line. His arrow went clean through the man’s throat. The soldier dropped, twitching once before going still.
Alec glanced back at Clary, calm even as the room burned around them. “Stay behind me. You’re doing fine.”
His tone wasn’t gentle; it was matter-of-fact, grounded. And for a moment, she could breathe again.
Jace called out from across the room, voice tight. “They’re regrouping. There are too many!”
Sebastian spun, his blades slick with black ichor. “We can’t hold this position.”
“Institute,” Alec said immediately.
Jonathan whirled on him. “We’re not going to your prison.”
Alec’s jaw clenched. “It’s not a prison. It’s a fortress. And it’s the only place with wards strong enough to keep her alive.”
“She’s our responsibility,” Jonathan snapped.
Alec fired another arrow so close it brushed Jonathan’s hair. The soldier behind him dropped dead. “You’re doing great at it so far,” Alec said evenly.
Jace’s laugh was quick and breathless. “He’s got a point.”
Sebastian wiped his blade on his sleeve. “Enough. The Circle will bring more. If we stay, we die.”
Jonathan hesitated, chest heaving, eyes burning. Then he looked at Clary, pale, trembling, blood on her hands that wasn’t hers and nodded once.
“Fine. But if this is a trick…”
“It’s not,” Alec said. “Move.”
They broke for the back exit.
The night outside was chaos. Smoke from the shattered wards hung like fog, and the streets were crawling with Circle scouts. The rain hadn’t let up; every drop hissed when it hit the runes burning on Jonathan’s arm.
Clary stumbled once. Jonathan caught her, holding her steady. “Keep your eyes forward,” he said roughly.
She wanted to ask where they were going, why they were running, what she was, but all she could do was move.
Alec led them through the narrow alleys, every turn purposeful. Jace guarded the rear, eyes scanning rooftops, blade flashing in the dark.
Behind them, the Circle shouted. A dozen voices, one wordless promise: You can’t run forever.
Sebastian looked back once, eyes narrowing. “We’ll see.”
Chapter 5: The Institute
Summary:
Quarantined inside the Institute, Clary meets the building’s calm menace and the Clave’s suspicion. Alec brings tea instead of threats and promises to stand with her when the questions come. Jonathan bristles, Sebastian measures, and the night ends with a promise: tomorrow, the Silent Brothers.
Chapter Text
The Institute did not breathe. It hummed.
Clary felt it in the soles of her wet shoes, in the quiet ring of steel from the training floor below, in the way runes shimmered faintly along the walls like veins of light. The building was not a place so much as a living map of everything she did not know.
Alec guided them through a long corridor lined with glass-paned doors. Each wore a thin film of witchlight that kept the hall the colour of a winter morning. Jace walked a half step ahead, casual on the surface, weight balanced like he expected trouble in the next five seconds and the five after that.
“Quarantine,” Alec said, stopping at a door etched with layered wards. “Temporary. It keeps the curious out as much as it keeps you in.”
Jonathan laughed softly. It did not sound amused. “A gilded cage is still a cage.”
“Then consider it armour,” Alec replied. He pressed his stele to the lock. The wards sighed and opened like a held breath let go.
Inside was spare and clean. Two narrow beds. A couch that would pretend to be a third. A small table with a carafe of water and cups. No windows. The walls carried sound oddly; Clary could hear the low pulse of the Institute through them, a heartbeat she could not match.
Sebastian stepped in first, checked corners by habit, then nodded once. Jonathan followed and stood just inside the door, a line of pale tension. Clary hovered in the threshold until Alec looked back at her, the set of his shoulders easing by a fraction.
“It is not much,” he said. “It is safe.”
She crossed the room and sat on the edge of the nearest bed. The blanket felt too new. The air smelled like soap and steel. She folded her hands to keep them from shaking and failed.
Alec noticed without commenting. “Someone will bring food. Tea, if you want it.”
“Tea,” she said, surprised by how quickly the answer came. “Please.”
He nodded and turned to go.
Jace lingered, gaze flicking from Jonathan to Clary and back. “Try to sleep,” he said to her, light and impossible. “Doctor’s orders.”
Jonathan took a step toward him. The air tightened.
Alec caught Jace by the elbow and steered him out into the corridor with the practised calm of someone who had been preventing bar fights since childhood. The door sealed behind them. Wards settled back into place, a soft shiver against Clary’s skin.
Silence.
Sebastian sank into the couch, long legs stretched out, eyes on the ceiling as if reading a language written in the plaster. Jonathan stood, then paced, then stood again, a storm contained by four careful walls.
Clary drank a glass of water she did not want. It tasted like nothing and steadied her anyway. When she looked up, Jonathan was watching her, expression unreadable.
“This is temporary,” he said. “We do not belong here.”
“I do not belong anywhere,” she heard herself answer, and wished she had not said it out loud.
Something in Jonathan’s face flickered. “You belong with us,” he said, too fast.
Sebastian’s eyes slid over. “She belongs where she chooses,” he corrected, cool but not unkind.
Clary lowered her gaze to her hands. The faint smear where she had dragged her fingers across the brick glowed in memory. That moment in the alley had felt like falling and being caught by something inside her that knew the ground better than she did.
The door chimed once. Jonathan’s blade was in his hand before the sound finished, but the ward shivered a familiar pattern and unlatched. Alec entered carrying a tray. Steam rose from a small pot and two cups. He set them on the table and stepped back, palms open, an unspoken promise not to come any nearer than the room allowed.
“Food is on the way,” he said. “I brought this first.”
Jonathan did not move. Sebastian did not either. Clary stood and crossed the short distance, poured tea with hands that were steadier when doing something simple. She offered a cup to Jonathan. He hesitated like it might burn, took it, and did not drink. She offered one to Sebastian. He accepted, a half nod for thanks.
Alec waited until Clary poured the last for herself before speaking again. “There will be questions,” he said. “From the Inquisitor. Possibly from the Silent Brothers. I will be present if you want me there.”
“You think we need a chaperone,” Jonathan said dryly.
“I think the Clave is better at breaking than mending,” Alec said, just as dry, and some of the iron in his voice bared itself. “My presence might slow them down.”
Clary found his gaze. The blue in his eyes was the exact colour of certain winter mornings when the sun was bright and the air held its breath. “Why help us?” she asked, not because she doubted him, but because she needed a reason that was not pity.
“Because you needed it,” he said simply, and then, softer, “and because none of this was your choice.”
Jonathan’s mouth twisted. “Choice is a luxury.”
“Sometimes,” Alec said. “Sometimes it is a fight.”
Footsteps passed in the hall. Voices, low and formal, moved away. The Institute’s heartbeat returned to its usual measured thrum.
Alec inclined his head to Clary. “If you need air, there is a warded balcony two levels up. Ask for me and I will take you. Don’t wander alone.”
“We are not children,” Jonathan said.
“No,” Alec agreed. “That is why I am telling you the truth.”
He left them to the tea and the humming walls.
They ate in fits and starts when the food came: soup that steamed in the cold of the room, bread that broke cleanly, fruit cut into precise slices. Clary’s appetite arrived in sudden, embarrassing waves. Jonathan pushed his bowl toward her when she reached the bottom of hers and pretended he had never wanted it. Sebastian ate like a man who had learned to never waste time with a knife and fork.
After, while Clary rinsed the cups at the little sink, voices rose outside sharp and rising, the kind of argument that did not care who heard. Jonathan crossed to the door like he meant to go through it. Sebastian caught his wrist without looking, the merest pressure.
“It is Jace,” Sebastian said. “And Alec.”
“Good,” Jonathan said. “I have a few words for your golden retriever.”
“And Alec has a bow,” Sebastian replied. “Measure your words.”
The ward pulsed, admitting a murmur of sound. Clary did not mean to listen, but it found her anyway.
“You brought them into the heart of the Institute,” a clipped voice said. “Lightwood, have you lost your mind?”
“I kept them alive,” Alec returned, even. “That is the job.”
“They are Morgensterns.”
“They are Shadowhunters.”
“And what will you do when they turn on you?”
“Be faster,” Alec said, and the door’s ward settled again, greedy with its secrets.
Clary exhaled. She had not realised she had been holding her breath.
“Try to sleep,” Sebastian said from the couch. “We will keep watch.”
“Do you sleep?” she asked.
“Not when it would be a luxury,” he answered, then closed his eyes without looking asleep at all.
Jonathan took the chair by the door. He cleaned his blade for the third time, then set it on his knee and stared at a point on the wall as if it would eventually blink first. Clary lay down on the bed and looked at the ceiling until the faint runes overhead softened into something like stars.
She did not sleep.
Later, the lock hummed and opened with the precise knock she had already learned to trust. Alec stepped in alone and stayed just inside the threshold.
“Five minutes,” he said. “If you want air.”
Sebastian opened one eye. Jonathan’s hand fell to his blade. Clary pushed the blanket back and stood.
“I will be right outside,” Jonathan said.
Alec’s mouth tugged, neither smile nor frown. “I assumed.”
The balcony was a narrow wedge of night tucked behind layered wards. The city spilled below, rain-slick and restless. The wards kept the wind out but not the smell of wet stone. Runes traced along the glass and made the air taste faintly of ozone.
Clary leaned against the railing, not touching it, just letting it exist near her and tried to swallow the knot in her throat.
“You do not have to do this,” Alec said quietly. “The questions. The Silent Brothers. Not tonight.”
“I should,” she said. “If there are answers.”
“There are always answers,” he said. “That does not mean they are kind.”
She looked at him. “Are you always like this?”
“Tall and miserable?” The corner of his mouth moved. “Only on Thursdays.”
A laugh startled out of her. It felt like a small victory for the day.
His expression warmed exactly one degree. “Tomorrow,” he said, business returning. “The Brothers requested an audience. I will go with you. Jace will be nearby. Magnus will consult.”
“Magnus?”
“Warlock,” Alec said. “Less annoying than he looks. Usually.”
The knot in her throat loosened. “Thank you.”
“You do not have to thank me.”
“I think I do,” she said. “Because everyone else keeps telling me what I am. You are the first person who has asked what I need.”
Alec nodded once, like he understood the difference perfectly. They stood in a companionable quiet. The city breathed. Somewhere below, a siren cut a thin line through the rain, then faded.
Back inside, Jonathan watched them return with the focused calm of a storm downgraded but not gone. Sebastian opened both eyes, satisfied when Clary walked past him under her own power.
Alec paused in the doorway. “Rest if you can. Tomorrow will be heavy.”
Clary lay down again. Sleep finally found her in fragments. In one, the alley rune burned bright and held. In another, a blade cut through smoke and turned into a pencil that would not stop drawing the same shape over and over. When she woke, the shape was still there in her mind, perfectly complete, waiting for a stele that was not yet hers.
The Institute hummed on. The runes on the wall breathed. Morning approached the way a shadow lengthens, quiet, inevitable.
And somewhere deep within those walls, the Silent Brothers waited with answers no one would like.
Chapter 6: The Silent and the Seen
Summary:
In the Silent City, the truth finally cracks open. The Silent Brothers reveal that Clary, Jonathan, and Sebastian were Valentine’s first experiments, his “children” of blood and rune. With Magnus and Alec at their side, the siblings begin to see that survival was never the whole story.
Chapter Text
Morning at the Institute never felt like a real morning.
Witchlight burned in the rafters, too even, too white; it didn’t warm anything. The city outside could have been midnight or noon, and Clary wouldn’t have known the difference.
She woke to the sound of Jonathan pacing. His boots tapped a steady rhythm against the floor, like a heartbeat that couldn’t decide if it wanted to live or fight. Sebastian sat by the door, perfectly composed, the kind of calm that came from control, not peace.
Alec arrived exactly on time. He never raised his voice, never moved faster than necessary, but every step was authority wrapped in quiet restraint.
“The Silent Brothers are ready,” he said. “The Clave wants their report as soon as possible.”
Jonathan turned on him immediately. “You mean they want proof.”
“Proof,” Alec agreed, “that you’re not what he made you to be.”
Jonathan’s jaw twitched, but he said nothing.
Sebastian rose smoothly, adjusting his jacket. “Then let’s get this over with.”
The descent into the Silent City felt endless.
The elevator wasn’t an elevator at all; it was a rune carved into the metal itself, lowering them through layers of stone and memory. The deeper they went, the more the air changed. It got colder. Heavier.
The silence wasn’t peaceful. It was expectant.
When the doors finally opened, the City stretched before them white stone walls carved with runes that breathed faintly under the witchlight. The air smelled faintly of dust and iron.
Clary’s pulse thudded in her ears. She tried to count her breaths, but the silence made every inhale sound too loud.
The Silent Brothers emerged from the mist one by one, their robes whispering against the floor. Their faces were covered by cloth and scars — eyes sewn shut, mouths closed with runes that still managed to speak.
A voice entered Clary’s head like a whisper beneath her skin. "Clarissa."
She froze. It wasn’t sound. It was thought direct, weightless, inescapable.
Alec moved slightly closer, his hand hovering near her shoulder without touching. “It’s all right,” he murmured. “They speak that way to everyone.”
Jonathan tensed. “Not to me, they don’t.”
The Brothers stopped in a semicircle around them. The one at the centre tilted his head toward Clary. "Child of blood and fire, will you let us see?"
Clary swallowed hard. “See what?”
"The truth you carry."
Jonathan stepped forward instantly. “You’re not touching her.”
The Brother didn’t look at him. "We do not touch. We only look."
Clary’s throat was dry. “If I say no?”
"Then we wait until you say yes."
Alec’s voice was gentle. “You decide, Clary. Not them. Not anyone else.”
She hesitated, then nodded. “Okay. I want to know.”
The Brother lifted a hand, palm glowing faintly. The air shifted. Clary’s vision blurred the stone walls, the witchlight, even the faces around her stretched and folded until everything became light.
Memories flooded through her like shards of glass: her mother’s voice whispering lullabies in a language she couldn’t remember; the smell of blood and fire; two boys, shadows at the edge of a cradle; a man’s voice murmuring stronger, stronger, they must be stronger.
Then... nothing. A wall. A blankness.
She gasped and stumbled backward. Alec caught her before she fell, his grip firm but careful.
“What did you see?” Sebastian asked, voice calm but tight.
Clary shook her head. “I saw... nothing. It stopped. Like someone erased it.”
The Brothers turned their attention toward Jonathan.
"You."
Jonathan’s eyes hardened. “Don’t start.”
"You were not erased. You were rewritten."
Sebastian’s calm cracked. “What are you saying?”
The Brother’s answer came like thunder that didn’t need sound. "He tested what the Angel made. Then he tested what the Angel would never allow. You three were the first lessons."
The silence that followed was a knife.
Clary’s stomach twisted. “The first...what?”
"The first children," the Brother said, each word a slow exhale. "Born of his hand, not of grace. The first to bleed for what he believed would save the world."
Jonathan stepped forward, shaking his head. “No. No, you’re lying.”
Sebastian’s voice was low. “He said we were chosen.”
"You were chosen", the Brother said. "Chosen to endure what others could not survive."
Jonathan’s breathing went ragged. “We weren’t experiments. We were his family.”
"You were both."
The words hit harder than any blade.
Clary felt something inside her crack like glass under too much pressure. “He experimented on us. On me?”
The Brothers turned back to her. "He began with them. He perfected with you."
Her vision blurred. “No.”
Jonathan spun toward her, eyes blazing. “He never touched you!”
“He didn’t have to,” she whispered. “He already did.”
The Brothers said nothing. They didn’t need to.
Alec broke the silence first, his voice steady but low. “We’re done.”
Jonathan looked ready to strike someone, anyone. “You think this means anything?”
“It means he broke you,” Alec said. “And somehow you’re still here.”
Jonathan’s fury faltered for a heartbeat, a flash of something wounded beneath all that armour.
Sebastian’s tone turned to glass again. “If the Clave already knows, what happens to us now?”
"The Clave knows parts. They never asked for the whole."
“And what happens if they do?”
"Then you will see what they are willing to forgive."
Magnus’s voice cut through the air like a candle flame in darkness. “That’s quite enough of the cryptic ghost story, don’t you think?”
He appeared from the mist, coat bright against the pale stone, eyes glowing faintly gold. “Honestly, Brothers, you have the worst bedside manner.”
Alec exhaled, relief flickering across his face. “You made good time.”
Magnus smirked. “I’m not late; you’re early.” His gaze fell on Clary, softening. “You, darling, look like you’ve seen the inside of a grave.”
Clary blinked back tears. “I think I did.”
Magnus studied her for a moment, then glanced at the Brothers. “If you’re done dismantling these children’s identities, I’d like a word with the living.”
The Brothers inclined their heads. "We have said enough. For now."
They drifted back into the mist, leaving the four of them five, counting Magnus standing in the echo of too many truths.
Jonathan finally spoke, his voice quiet and broken. “He made us. Every part of us.”
Sebastian answered without emotion. “And we’re still here. That’s what matters.”
Clary looked between them. “No,” she said softly. “What matters is what we do now.”
Magnus arched a brow. “Spoken like someone who doesn’t yet understand how hard that question really is.”
Alec reached out, resting a hand on Clary’s shoulder. “We’ll figure it out. Together.”
Jonathan’s eyes narrowed at the word together, but he didn’t protest.
As they made their way back toward the lift, Clary felt the city shift beneath them as if the stone itself knew what had been uncovered. Every step echoed. Every rune they passed seemed to hum louder.
She couldn’t shake the word the Brothers had given her.
"Children."
Not weapons. Not soldiers.
Just children broken before they ever had a chance to grow.
And now, for the first time, they weren’t hiding anymore.

Emily_M_Brook_Nerd on Chapter 1 Thu 11 Sep 2025 04:52PM UTC
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Darkling098 on Chapter 1 Thu 11 Sep 2025 07:42PM UTC
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HerikadoBrasil on Chapter 1 Sun 28 Sep 2025 12:33AM UTC
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HerikadoBrasil on Chapter 3 Sun 28 Sep 2025 12:43AM UTC
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HerikadoBrasil on Chapter 6 Sat 11 Oct 2025 06:28PM UTC
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