Hey guys, first try at The Mortal Instruments fanfic. Hope you like it!

City of Heavenly Fire AU. What would happen if Jonathan had not burned out from Clary's flames, and instead happened to wake up confounded in a dark cell, having to deal with the atrocities of his previous crimes and to face a new, lighter side of himself?

The throne seat Jonathan relaxed in was large, his back comfortably sunken down on pillows embedded in some soft material; silk most like. Or linen? Jonathan had a distant memory of picking them out especially for this occasion, wanting to give an elegant style to the previously plain throne; dark crimson achieving its desired effect of making the seat look, if possible, more threatening.

Undoubtedly a seat for a king, no, a leader; a feared and respected leader.

Jonathan could look down on his subjects from up here, show them his superiority. The throne was a simple reminder that everybody who doubted him was wrong about his failure, wrong about him.

On his white hair a crown lay, a crown of royalty, a token and reminder of his victory.

Flames reflected in his wild black eyes, flames of the world burning down as he looked up in satisfaction from his seat; innumerous screams like a symphony in his head.

His world. His new creation. In some ways, he was like a god, an improved one, if he was one for judgement. The world was his, Clary, who sat next to him with an equally beautiful crown on her red curls, was his as well. She was his queen, and together they would rule their kingdom, or live long enough to watch it burn in the process.

The thought made him smile despite himself. Considering the circumstances it even felt somehow genuine, but as Jonathan previously figured out, the world doesn't like to gift him with genuine things.

As if sensing it before it actually happened, a ragged cry was constricted in the ruler's throat. The solid platform that once held him steady gave way, a work intricately constructed of iron and copper collapsing upon itself piece by piece as the pillows dissolved into ashes, and the metal scattered broken on the ground.

A ringing sound was loud in Jonathan's ears and ashes a bitter taste in his mouth.

Now without support he felt himself falling, desperately trying to cling onto thin air, even as the flames faded and his vision darkened.

"Jonathan!" A voice screamed. "Jonathan, my sweet brother, where are you?"

Jonathan frantically tried to search around him, he seemed to be momentarily suspended in darkness, no light showing way to the voice calling out for him.

"I'm here," he yelled breathlessly. "It's too dark to see."

Unexpectedly a sudden warmth enveloped him, and Jonathan found himself wrapped in an embrace with the person he was searching for.

"Clary?"

"Why did you do this?" She now seemed to be crying, her face slowly being illuminated, a few salty tears staining her cheeks. "We could have been happy, but you wanted it all, didn't you?"

"What do you mean?"

"The throne, the world, burning it all to ashes like you would've burned me to reach your ends."

Jonathan wanted to snap at her, to tell her how much bigger any of this was than her, how he worked hard for this and would never have to weigh his dream over her life, about to tell her how puny and small she truly was. But even as the words tracked his mind, he started wavering; feeling a resoluteness he hadn't felt before. Suddenly, in a strangle of fog that cleared his mind, Jonathan didn't really remember what was the purpose of his plans anymore, why he had condemned so many people to the grave. His heart lurched in pain and he felt himself tremble, remembering himself laughing as he spilled the blood of Shadowhunters and Downworlders alike, carefree in his judgement. Was he wrong to do so?

Biting his lip hard enough so to draw blood, Jonathan felt himself grow cold once more, his laugh coming cruel and booming while they both were suspended in what seemed to be his mind's limbo.

"You always know where my priorities lie, little sis."

He roughly grasped her, digging his fingernails into her shoulder blades hard enough to bruise. He enjoyed the way she squirmed under his firm hold, her enmity back, and her eyes defiant as he kissed her and she spit vehemently in his mouth in disgust.

For a few blissful moments he was entangled in her, and her eyes drooped just the slightest, and her biting grew more infrequent as she relinquished some of her power.

Whilst his mouth fought to keep his control over hers, he felt a heat radiating between them, Clary's muffled screaming in his mouth as fire began to catch on her. Her face melted in flames, a morbid, scorched look staring back at him. Her screams grew distant as she disintegrated, flames torching her skin as if it would a cloth, slowly but powerfully until everything turned to ruin. The burnt taste of ashes again stained his mouth, and with a choked scream, he felt himself being drawn back to consciousness.

Jonathan woke up distressed, breathing heavily, chest heaving, his body soaked in cold sweat from his nightmare.

Every inch of his body seemed to tremble at the memory, and in place of ashes, he only felt disgust. He swallowed weakly, letting his tongue roam hesitantly over his lips.

The lips he dreamed were kissing his sister. Clary. His... Sister in blood. His face twisted in horrid realization. In his dream, his conflicted halves battled, and his darker half won, and that side of him seemed to enjoy the feel of his sister's tongue fighting his own, the feeble attempts at defiance only thrilling him more.

Shocked, he raised a hand, as if searching for some remnants of a crown nestled in his hair.

He only made way halfway before he got stuck. Only then had Jonathan noticed that his hands were confined in chains. Once pulling himself to a seating position, he heard a metallic sound, letting him know that his legs were chained as well.

It would be best if you refrain from sitting up, please. A sudden voice appeared in his head. He turned his head right, and was met with the presence of one of the Silent Brothers. It took him more than a few seconds to piece together what had previously happened, memories suddenly clear as he retraced the event. Jonathan's heart hammered in his chest. Clary's sword in his heart. Why hadn't he died? How did he get here?

"The Clave required you to t-torture me before you kill me?" Jonathan asked, his voice unexpectedly breaking.

It wasn't like him to lose control over his own voice, Jonathan had always remained composed, his voice was either hard or smooth, but never broken; never hesitant. A lesson his father taught him well.

Father told me that you're only as confident as you sound. Showing weakness verbally or physically will turn the person in himself weak, he had told him. Every time he mumbled, trembled, or had tears hidden in his eyes, his father would discipline his child, usually with the help of a whip. Other times with the help of words.

Trying to regain some upper hand, Jonathan lowered himself from his bunk with a jump, surprised to learn that the chains on his feet and arms gave him the space to do so.

The Silent Brother moved silently towards him. Sebastian, I fear that you must return to your place. The Clave has required that I must use force if needed in order to contain any disobedience, force you might find unpleasant.

Jonathan gave the Silent Brother an inquiring look, and with a defeated sigh, returned to his bunk.

"My name is Jonathan, by the way," he said casually.

The Silent Brother didn't linger long, and soon Jonathan saw him make move to leave through the door.

Wait in your place. Don't move. The voice of the Silent Brother sounded in his head, and then with silent footsteps, he left the room.

Jonathan studied his surrounding for a few minutes, finding the spacious room seemingly empty despite the bunk he was laying down on and a flickering light that kept only a small space bright enough to see in. Although unable to see beyond, Jonathan had a strong feeling that more equipment was hidden in the darkness, and that even now, eyes were on him.

Alternating to staring at the ceiling, Jonathan started thinking.

He remembered what happened. He remembered how everybody bowed to him, well, everyone except Jace. But how did he get here? Is it possible that he died? Was hell truly this... similar to his world? He closed all the gates back out, so it shouldn't have been possible to have survived this. Even if by some miracle the sword that struck him hadn't sent him straight downwards to hell, surely Clary and the others would have put an end to it.

Jonathan felt an odd sensation, as if his blood had been purified, an odd sense of remorse taking place where seeking vengeance and battling for domination used to reside.

He almost felt something akin to... fear. It should have disgusted him, after all, Valentine had worked meticulously to squash these pestering feelings out of him, tried to make a... monster out of him? No no, Valentine had wanted to make him strong, to make him less pitiful than the others, to train him with the skills of a leader.

Did he lack as much compassion as Jonathan had? Had raising him like this been... wrong? He never seemed to think so, but now his head convulsed in itself and he could hear screams, distant but fathomable, the people whose families he probably ripped apart.

How could he have been so blind? Did he truly think Clary would be capable of loving him after everything he'd done? Or did he think forced, manipulated love was the best he could get without ruining his plans?

Suddenly feeling wearisome, Jonathan closed his eyes, and a few seconds later opened them, hoping for once that he was truly dead and this was only some hallucination before his judgement.

The room was still as dark and empty as before, a few droplets of water leaking from ceiling to create a repetitive splashing noise, one that matched the quiet rhythm of his breathing.

Subconsciously he reached for his bracelet, to twist it around in his fingers to keep his mind from wandering, only to realize it wasn't there.

Instead, he bit his lower lip. Better the taste of blood than the taste of ashes, or the bile that threatened to go up his throat at the thought of him forcing himself down on his sister.

Besides the pain helped him think, helped him understand himself better.

Assuming he actually survived, which seemed to be the probable answer, why not kill him straight off? Why risk him gathering his strengths back and causing more harm? Is the Clave planning on torturing him, making him atone for his previous crimes before finally getting rid of him?

The door opened in a screech, snapping him back to his reality; the cold reality of being stuck in what appeared to be a dungeon, with his captor having full access to do whatever he desired to do to him.

It took a few moments for the blond to show his face, as if he was hesitant if to enter or not.

It was unmistakable who that blond was.

Jace.

Jonathan's heart pace quickened at the sight of him, and it took all his courage to swallow the unfamiliar aching fear, and make a turn to sit upright on his bunk.

In the corner of his eye, he spotted Jace's hand curled tightly around his sword, and with a sinking feeling Jonathan knew that it was meant for him.

He was going to kill him. Or at least make him agonize until he does.

Breathing became harder. To die by your strikingly handsome adoptive brother once is one thing; dying by the same hand a SECOND time is likely to paint the Morgensterns as a quite dysfunctional family. Throw in a hateful sister, an abusive father, a guilt driven, murderous mother and you got yourself one amusingly colorful family meal.

That was if Jace ever acknowledged himself as a Morgenstern, which he doesn't.

Either way, dying didn't really appeal to Jonathan.

"Jace-" he began to say, and quickly regretted it.

At the sound of his voice, Jace lifted his weapon and pointed it towards Jonathan's chest, unflinching. Cold, dark malice was hidden in those golden pearls, and now with the ability to sympathize, Jonathan knew that it bore true hatred for him.

"On your feet." Jace commanded of him, his tone a match for his cold, hard eyes.

A chill crept up Jonathan's back and he awkwardly stumbled on wobbly feet.

He hates me, he thought. He hates me and he's going to kill me. Like I killed Max.

Jonathan, once being quite curious about the ways of physical torture, knew that predicting what was about to come next for him was going to be impossible.

Jace seemed like an old fashioned sort of guy, but Jonathan was convinced that the blond was under strict orders, and the Clave would want his death to be a painful one.

Perhaps Jace would start out by cutting his fingers and come back an hour later to cut out his tongue? Maybe he would like to carve a drawing with his sword on Jonathan's pale, tingly flesh and afterwards, once Jonathan would be an incorrigible, weeping mess on the ground, void of various fingers and swollen of cries, Jace would finally give him the mercy of a quick death?

Jonathan had always suffered from an over active imagination, or maybe it was the newfound paranoia he was experiencing.

"Give me your hand." Jace spoke, and Jonathan did as he was bid.

Ah, so they would have him cut off his hand first? Just like last time? How morbidly ironic. Jonathan felt himself regretting offering him his right arm on instinct. His good arm.

Jace took hold of his forearm with both hands, leaving the rest of his arm uncomfortably exposed as he was made to stretch open his hand.

Jace's hands were hot on his flesh, as if steaming from rage. He lowered his dagger to Jonathan's skin, who awaited his fate. He only wondered if the ministry would give him enough time to get used to a life without a hand.

To his surprise, Jace only lightly grazed his skin with the dagger, leaving a scratch small enough that one could think an angry cat had left the bruise with sharp nails. A few crimson droplets of blood fell from his arm and onto the shiny, stone floor.

Jonathan raised his head to give Jace an inquiring look, almost screaming for him to stop teasing and rip his arm from his socket if he so pleased, but Jace only stared at his forearm, as if waiting for something to happen.

When nothing did, he wrinkled his nose. His features softened the tiniest bit.

"You have a few minutes to get ready, prepare".

The dagger which he had cut him with was sheathed back to its place, whilst Jace marched in quick steps towards the door. He opened it, lost in thought, and that's when Jonathan called after him. "Wait," he said and Jace paused momentarily, but not turning his way towards Jonathan. "Where am I going in a few minutes? Am I trading confinements"?

"Ah," Jace curtly replied, taking another step out the exit. Jonathan vaguely noticed that Jace never made eye contact with him since he cut him, oddly enough. "That we might find out soon enough." He ended the conversation with a smile that Jonathan didn't see, slamming the door on his way out.