An alternative ending starting with the events of episode 9, and going AU after that point and onwards.
I do not mean any copyright infrigement, and I hope you will like my story.
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Jace thought his heart couldn't break into more pieces, having to fight his parabatai, then, as they both regained their senses, and Alec still didn't... no, he was no aware that a shadowhunter's heart could be broken into so many pieces, let along keep beating. He had thought it was Clary who was all heart - turns out his' could hurt this badly, too.
As Alec walked away, Jace remained seated on the ground. He hadn't meant to lash out with his words in the way he had done, blaming Alec's sudden whatever-it-was for his behaviour, but he had been at the end of his sanity by the time he said those things. And now, he had to pull himself together and find the two others, ignoring the sudden pain at the knowledge that Clary had replaced Alec in that equation. He couldn't break like that now. They had work to do.
The next few hours were intense. Izzy had gone back to the institute to see what information she could gather there, only to have to flee at a moment's notice to narrowly avoid arrest. It was only due to Magnus' foresight in making her a once-only portable portal-opener and then acting quickly once she needed it that she was not caught. She could not go back to the institute or any other place under the Clave's control any more than Clary and Jace could.
They were all made welcome though at the court of the Seelie Queen. Over the next few weeks, Isabelle especially fascinated quite a few of the ladies-in-waiting, perhaps because most of them had failed, at some point, to attract the attention of Meliorn. It seemed Isabelle's Seelie Knight was not easily seduced. Jace felt a bit proud of her, perhaps irrationally.
They spent the time starting to cement the still fragile alliance between vampires, werewolves, warlocks and seelies. The warlocks, following in their guardian, Magnus', example, got along fairly well with all groups, especially the seelies, and - mostly after some efforts made by Luke and Meliorn - werewolves and Seelies found common ground in how their special senses linked them to the earth and nature.
The vampires, too, accepted the seelies with only a minimal amount of fuss - though the seelies themselves were somewhat more unwilling, sharing the werewolves' aversion to "dead things" - but it was, like expected, the relationship between vampires and werewolves that took the most effort and needed the most work - from all of them - to not blow up in their faces.
As they welcomed more downworlders from more places, Raphael's dutiful courtesy with Luke, and Luke's playful teasing of a Simon who lost control and had his fangs out, came a long way to prove it was possible.
In an effort to further cement that they were all downworlders here, and nothing else mattered, Isabelle and Meliorn were wed together in a seelie ceremony.
It was at their wedding festivities, Isabelle looking resplendent in a silver gown and Meliorn dressed to match, that Magnus arrived in his signature fabulous flurry with news.
"Please say that this is not bad," Isabelle asked, pausing from her night of dancing. Everyone - seelie, werewolf, vampire, warlock and shadowhunter alike - had stopped to pay attention to the High Warlock of Brooklyn. "No. It is good," Magnus assured her in a smug voice. "Valentine had a new plan - and I stole it," Magnus gestured widely in his flamboyant manner, looking very pleased with himself. He looked over to Clary, standing against Jace, who was holding a protective arm around her waist.
"Valentine had a son." "We know that," a seelie responded impatiently, "the boy died in a fire." "So did Valentine," Magnus reminded them, a self-satisfied smirk on his lips. "My brother is alive?!" Clary looked and sounded like she didn't know whether to be pleased or horrified with this revelation.
"No, Biscuit," Magnus turned back to her, his face grave. "Valentine got them both away from the fire, but the child suffered grave burns. That coupled with the demon blood," several gasps of horror were heard at that, "lead to his demise, in the weeks which followed. But Valentine," the warlock's eyes narrowed imperceptibly, "plans to claim that it is Jonathan", this time the pause was merely for effect," who is your brother." Clary blinked, Jace squeezing her towards him slightly. "What? Why would he do that? If it isn't true..."
"Valentine is a liar, Biscuit. He lies," Magnus reminded her, his eyes fond as he pronounced the nickname. "Because this," he gestures towards her and Jace, who was still holding her close, keeping her safe against his own shoulders, "gives you strength, and he wants to take that from you. But it is a lie," the warlock announced the word decisively, "I have proven it. We have gotten one step closer, to be ahead of his game."
"So Clary doesn't have a brother," Jace decided to get this confirmed. Magnus looked back at him with all the derision any responsible father would feel at his daughter's boyfriend, though he was not aware of this fact. Like for Luke, Magnus' bond to Jocelyn and loyalty to her family ran deep in the warlock. "She did, but he is dead. You, too, have a brother, but he is a..." Magnus made a vague, annoyed gesture with his hand, drawing an irritated breath. "Hey," Isabelle's voice was playful, "don't say anything bad about Max!" There were a few laughs greeting this statement. The warlock's eyes softened. "Never would I ever," he replied gently, smiling.
"I hate myself for asking this," all eyes now turned on Simon, instead, standing between Luke and Raphael, bridging the gap between several vampire covens and werewolf packs, "but are we absolutely sure Clary was never... by her father...? Demons?" He grimaced. "That's alright, Simon, everyone was thinking it anyway," Clary answered with a grimace. "Yes!" Magnus responded a little too dramatically, even for him, as well as a little too loudly. "We are sure of that!" He looked at Clary with understanding in his suddenly catlike eyes.
"Your mother fled from Valentine the moment she did for many reasons." The warlock's voice was tender, and hie eyes caring as he addressed Clary, speaking loudly enough for them all to hear him. "She was aware of what your father did to your brother, only too late, and she got you away in time, Biscuit. Before he could touch you in any way. She had me check at your birth, and again and again as you grew, though I couldn't possibly have missed it the first time. There is nothing wrong with you, nothing, and yes," his eyes swept over the - relieved rather than sceptical - faces surrounding them, "I am absolutely certain." "Thank you," Jace's words were not expected, but Magnus looked like they were satisfying.
