At the end of City Of Heavenly Fire, Sebastian did lose the war but as a result, Jace ended up being bitten by a demon and transformed into one. When they were transported back to Idris, Clary and the gang couldn't bear to kill him and as a favour from the Clave, they agreed to have him kept in Magnus' pentagram in the hope that one day they could save him.
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-InfernoAlive
My Evil Angel
Clary bit her lip as she walked with Isabelle, clenching and unclenching her fists, as tears threatened to fall in her eyes. As if she sense them, Isabelle pulled her close and held her against her chest as they walked. Passers-by didn't notice them because of the Invisible Rune inked on both of the girls' arms, but it seemed the whole of Brooklyn was staring at her, taunting with malicious glee.
"That's Jonathan Morgenstern's sister…"
"Valentine's daughter… sinful family…"
"Scum! The lot of them! Even that Jace Herondale…"
Jace… Clary gulped and this time the tears fell free, streaming down her face like an endless river. She could still remember the scream Jace had let out, the cry of agony as his back arched back like a bow about to shoot an arrow. She'd run over to him amidst the battle of demons her brother had conjured, and tried to tear the creature that clung to his neck, biting down savagely.
"Clary! Run! Save your… self…"The way he crippled to the ground as the demon evaporated, and slumped like a weak, injured animal. Jace, who was the strongest person Clary had ever met.
"We're here, Clary." Isabelle whispered to her, but Clary could barely make out anything as the misery tore through her heart. She knew where they were: the dwelling of Magnus Bane, High Warlock of Brooklyn. The place where the Clave had agreed to keep Jace.
They walked through into the house and met Magnus into a dimly lit corridor, the blue fire of a wall torch creating eerie shadows on all their faces. A door lured ahead and from inside came the wobbling tune of Shakespeare…
"Oh come now, thou see the beauty I stare in thou art face, of beauty and dignified justice. Let thou cleanse all beauty and leave none art but blank… Hear thee!"
Magnus, reduced to but a sprinkling of glitter, met Clary's gaze gravely, "He's been going on like that all this time, speaking of ruined beauty and all that larky poetry."
Clary gulped, remembering how Jace used to sometimes quote lines at her, how it made her annoyed, sad, happy. How it made her fall in love all over again.
"Has there been any changes-" Isabelle began but was cut off by more warbling.
"Sister mine, thou tastes tenderly sweet shall your tree grow ripe and lovely to behold! Cease the barren that once was…"
"No." Magnus had to raise his voice above Jace's passionate cries, "And it's beginning to piss me off!"
Isabelle's hold on Clary tightened, and she whispered, "Would it be possible if Clary could see him?"
"I don't know, he's not really his best right now, compared to the arrogant, pretty boy he once was." Magnus shrugged and studied Clary pitifully. That pity made a fire grow in her heart and she could not stand it anymore.
"I'm not asking Isabelle. I am going to see him. Do you have a problem with that? Magnus?" She hissed his name, narrowing her eyes as she watched a flicker of admiration cross over Magnus' face.
"All yours biscuit," Magnus gestured towards the door, and without a thought Clary shook off Isabelle and opened the door.
The wild quoting got louder as she entered before closing the door behind her. She was in a round room with quite a low ceiling. The room was lit up with blue wall torches, and with the shackles and manacles hanging from the walls she got the impression she was in a dungeon. In the centre of the dungeon was a pentagram, glowing black and red as the creature within writhed in pain.
Not creature, she reminded herself fiercely. Jace.
He didn't notice her at first, with his head down so she couldn't see his face. He was in the same battle clothes she'd once seen him in, but they were tattered and hanging from his body in ribbons. His blond hair glowed golden amidst the darkness, and all the locks waved, like rays of sunlight.
"Come cleanse my sins, and give me heaven!" He suddenly shrieked, making Clary jump in shock, "Give me innocence to cut out my guilt, and foresee the angel's cry so I might strike. Hand me one of yours from above and I will hand you mine."
She gasped as she took in Jace's torturous words, and his quoting came to a stop. Slowly he lifted his head up, his hair falling in his face and stared at her. She stared back. His face was the same as she'd remembered it, angular and perfect; his sculpted lips as soft as she knew. But his eyes…
They were as black as coal, as black as her brother's. As black as a demon's.
His lips stretched into a twisted grin that sent a shiver down her spine and his dark eyes gleamed with an evil light.
"Thou from above, May I bless with a hand of righteous sin and strike thou art with a blade of both lands?" Clary was rendered speechless, taking in Jace's words with fear. Did he intend to kill her?
The grin wavered on his face, then fell completely, making him look calm but dangerous – Clary swore her heart stopped for a second. Then he cleared his throat and announced in a dark, very un-Jace-like voice, "Kill me now."