Notes:

It is true in the past I've had some issues updating other stories, its why I took a long break from fanfiction before returning with this story. This show has really been a thought-sparker, so…of course when I'm in groove, real life likes to remind me it exists. My grandmothers both had health crisis within hours of each other, they live in different city and neither live in the city as me. To top it off there was a holiday (Purim) for which I had obligations, as well as a couple other things so I had to temporarily back burner writing. But I am back and I appreciate your patience.

This chapter is shorter than I would have preferred but I wanted to get something up, so this is what I had before I had to focus on other things. I mostly didn't finish the portion of parabatai explanation and a bookend flashback featuring Gideon, Izzy, and Jace about Jace's first day and how two Jonathans became Jace and Gideon. Hopefully, now that life has calmed down I will get that up by the end of the week. Also as a thank you and an apology for the huge game I'm also posting a deleted scene from the last chapter I had to chop a bit, its Simon, Alec, and Clary first 'playdate' so to speak.

Luke walked up the stairs with a slight sense of concern as to what he might be walking into as he heard the shouting carrying across the entire building. He looked to where Dot was maintaining her position behind the counter, but she only shrugged her shoulders with a sympathetic smile.

"Alec, I am your mother...you don't ever speak to me like that." The police officer recognized the tone in his wife voice as stern, but exasperated which made him wonder how long this argument had been going on before he arrived.

"Mom!" Clary was chiming in.

"Clary...this isn't your fight…" Alec's voice was clearly angry about something as it got louder along with the sound of wheels against the wooden floors. As Luke arrived at the the top of the stairs he could see the thirteen year old roll directly for the elevator, Jocelyn just far enough behind him that he managed to get the door pulled down in time.

"Alexander. Christopher. Garroway." She turned to head towards the stairs, but spotted her husband. Her shoulders collapsed as she approached…

"He got in a fight today during archery club…I'm just worried...he's been so angry lately…"

Luke nodded, understanding as he shared her concern, "Let me go talk to him."

It was a long moment before he got the nod of approval and turned to go back down the stairs. He paused to let the boy get a good slam of the downstairs door before he finished the last step and followed outside.

Alec hadn't made it far, stopping just before the turn that led to the street.

"Come on, let's go...you need to spin this out."

They pair went along in silence for a block or two before Luke felt like it was safe enough to breach the topic. "You're not usually the fighting, angry, secret keeping type…"

"Maybe I'm starting to learn from you and mom…"

Luke stopped in his tracks and with a quick grab stopped Alec's chair from moving any further, "What's that supposed to mean?"

"It means I'm thirteen not stupid, Dad! I hear you two talking at night….Who is Jonathan? If Clary looks like mom, do I look like our birth dad? Where did we live before this? Why do you guys never answers the questions?!"

He took a deep breath, and took over pushing the wheelchair in silence. He didn't know if it was to prevent Alec from taking off again, because they needed to get away from the people filling the sidewalk, or because he was buying himself a little time to come up with answers; he tried to convince himself it was probably more so the latter. As they approached a thinly populated space of sidewalk he pulled his son over and stepped in front. With some amount of control he lowered himself down until they had reached eye level.

"You're right: you are not stupid...but you are thirteen." Alec's face began to twist but Luke carried on regardless, "You're starting to figure out who you are and what you really want to do when you grow up, you're becoming an adult and you're becoming aware of the world around you. There's a lot you're going to learn….but you're mom and I don't want you become an adult too fast, you still have a lot of things to enjoy too, okay? One day, you will get all the answers, you just have to trust us know when that can happen, okay?"

It took a while of Alec's eye locked on his before he got a slow nod. There was a sense of relief that they answer, though not the best he could have given seemed to work. He and Jocelyn would have to be more careful if they wanted to avoid having the conversation sooner than they were ready. Maybe it was selfish of them but he really loved this version of reality; where he could spend time away from the pack as a normal human, with a life, where he could forget about the past.

"So, tell me about this fight?" Lucas changed the subject abruptly and laughing as Alec groaned.

Reunited with his chair Alec was happy to roll away from Jace who still seemed to be extremely focused on whatever he had seen, thought he saw on Alec's back. He followed Luke with Clary and Simon to the elevator and to the upstairs. This place as whole had so far been an odd, yet bright clash of modern technology and classic architecture. However, the room they had just entered had a much different feeling then the rest of the building, but the details were lost on Alec as he carefully watched his dad head to the opposite side of the room to stare out the window.

His sister's eyes darted between the men in the room. Her dad was focused outward, her brother was focused on their dad, and only Simon looked elsewhere. Her childhood friend was sending her what she was sure he meant to be reassuring smile but only came off as standard Simon-goofy. It was still comforting, something that in this midst of this night was still the same.

The quiet filled the room for a long while as if no one was quiet ready to tempt the task of breaking it.

Silence seemed to be the theme for the evening as it also hung thickly in the infirmary where Isabelle, her brothers, and Magnus were trying to process their side of the information. Jace stared in the direction the others had walked, shaking his head. He started walking, determined to find his answers, but he was stopped by a hand wrapped around his arm.

He suspected to find the hand belonged to his older brother, however Gideon was focused on the floor under where he was sitting on a bed next to Izzy. It was the warlock who had stopped him and he pulls away fairly quickly at that realization going to join his siblings.

"I don't understand how he could be…"

"I don't understand why your so upset." Magnus muttered in a faux quiet, cleary not concerned with who did or did not hear.

Izzy just shook her head, "I just don't understand any of this…how do…why they hide in the Mundane world when they are Shadowhunters?"

The quiet tempted again but once again the warlock spoke up, "Maybe if you remembered what it was like back then…"

" The Shadowworld has never been quiet as progressive as the mundane…the human world." Luke's voice carefully broke into the room, but he stayed focused on the window. "There was always been a strictly enforced hierarchy, a segregation between the Shadowhunters…those half human, half angel defenders of the humans and the Downworlders.."

Simon began to speak up, "Down…"

"Vampires, fairies, werewolves. Warlocks…."

Luke finally looked at the three young adults to find varied responses. Simon looked like he was in a dream; an exciting, but slightly terrifying dream. He had seen that look on Clary's face enough to know she was on information overload. Finally he looked at Alec who's face was staring straight faced back at him, as if he was accepting anything so nothing could shock him.

"Anyhow after centuries….tensions were rising… around the time Alec was born things had started coming to a breaking point. A Shadowhunter named Valentine Morgenstern became the voice against the Clave, the governing body of Shadowhunters….he argued against the Clave, and convinced a lot of people that there could and should be change…his Parabatai included…"

"Parabooty? That's the word that Jace guy kept calling Alec?" Simon piped up, Luke passingly thought he was probably the only once processing things at a functional level to interact, his self-proclaimed nerdy tendencies might actually be working in his favor, for once.

"Parabatai." The older man corrected, "Shadowhunters have a lot of runes, but there's a couple marks that we still don't fully understand, and one of them is the Parabatai mark. It doesn't happen to everyone but when it appears from birth….

"But ours…" Alec started….

His dad just shook his head, "We'll get to that in a moment...you still need to understand who we thought Valentine was..."

"We?"

"Jocelyn had married him young, enamored with his ideas for a better world...stood by his side, like I did when he started converting others to our cause. We were the start of what Valentine began to 'The Circle'..."

"So the werewolf was not only a Shadowhunter, but Valentine's Parabatai? That man helped one of the most rogue Shadowhunters…."

Magnus was already cutting Gideon off, "Luke saw the truth before anyone else. He and Jocelyn realized that he was trying to weaken the Clave only to take over and control the Shadowworld…and clearly not in a good way. True, we know the Clave was wrong in a lot of what it was doing, but what Valentine wanted was worse. His secret master plan was to steal the Mortal Cup… and along the way he orchestrated so many deaths disguising them as the Clave or as Downworlder revenge kills."

Magnus shudders silently at the memories he's rarely pulled forward. The three Shadowhunter siblings waited for him to continue, they were used Magnus' usually vibrant personality. His eccentricities were something they had come to accept growing up in the New York Institute, learning from him, working with him. But this seriousness on the warlock was something they had not experienced before.

Izzy seemed the most intent to understand and was using the time to think for a moment. "How did Luke become a werewolf?" She asked, afraid she might have already have guessed the answer.

"He had apparently figured out Jocelyn and I had discovered the truth…and he decided the pain of destroying the bond was worth it for his plan. Even if we hadn't figured it out I don't think he would have let me live for too long anyhow. He was getting paranoid as Jocelyn and I spent more time…" He shrugged a little as if in response to a fleeting thought in his own head, "He was getting paranoid about everything. I knew something was wrong, but I guess I hoped…

"He told me there was a werewolf…rogue, who needed help the next thing I knew I was locked in a barn…and…Jocelyn stood by me the whole time. We knew then we had no choice."

Luke had gone back to staring out the window, at the sun that was starting to creep on the edge of the horizon. He had been a Shadowhunter, had survived Valentine, and was now entirely afraid of what the children he raised would think of them, sure they were slowly putting together the pieces.

Alec who had been quiet interrupted his dad's silence, "You said this was about the time I was born..."

"You were safe…hidden with a family friend." As far as he knew it had been the truth. He knew the full truth was going to come out especially now that Alec was inside of the New York Institute. Still, he wanted Alec to have something to hold on, even if only for a little while, while he processed the new world that had emerged around him. "Who a Shadowhunter was, who that had to be had strict rules, and when you were born, there were a lot of people who didn't believe you fit. Unfortunately, you will still find people who believe that."

Alec nodded slowly, looking to the floor, his nod meant for himself as he seemed to relapse into his quiet state of processing.

"And me? When did Mom find out? Did Valentine?"

Luke looked to at Clary, met her eyes with a long stare, "Jocelyn never told him, but I suspect he may have known. After he believed he killed me Val kept her extremely close…"

"So how was he stopped?" Simon's enthusiasm had settled down, turning into a sympathetic support he was trying to lace with an appropriate level of concern to hide the millions of questions that popped in his head as Luke continued.

"Valentine believed the attack had killed Luke, but Luke had survived. He was just different, now a Downworlder. It proved to be Morgenstern's downfall. Luke could now move around and garnered alliances he would never have managed as a Shadowhunter. Jocelyn Fairchild kept cautiously plotting from the inside of the circle.

"The victory came when Valentine led his followers to steal the Mortal Cup...he had not suspected that instead of the Cup, he would find a small army of Downworlders who now knew he never had any intention on a united world. They attacked...a number of members of the Circle ran, few of those who stayed survived the battle that followed."

Gideon was now uncharacteristically pacing between two of the infirmary beds, before he slowed, "Who killed Valentine?"

"Jocelyn did. She was probably the only one who could have and she had more right than anyone else there...including Luke." Magnus spoke those words carefully catching Jace's opening mouth with his last two words.

He had miss guessed the boy's question, "Were you there?"

The warlock took a long time with the question. It seemed, from intent he was being starred at a rather important question. These three had been raised and trained to look at every attack and every possible solution from all its angles. Magnus had refused to speak of this era with a lot of detail for many reasons to those of the New York Institute. "How do you think I got this position?"
It was all he would say to the question.

"After Valentine's death...the Clave, severely exposed and weakened by The Circle over the years tried to reclaim control through their old tactics. There executions and punishments, not all of which met the crimes. They held no regard that the overwhelming majority of the member, especially those who had ran from the last battle, had no idea of the extent of Valentine's crimes.

"They wanted to make examples of Jocelyn and I, despite calls from Shadowhunters for a pardon as we had stopped him. The Clave was stubborn, and refused to adjust any of it rules...more fights broke out. Leaving was the only option. Through some contacts we were able to secure some finances and alias' for us and you so that we could all escape to the mundane world. We didn't think we would ever be able to come back, and we feared some of the Circle members who might survive the Clave's wrath. We really thought it would be safer to hide you from the Shadowworld. With the help of a warlock we gave you both blocking runes." He moved his hand to his own collarbone, silently referencing what he was talking about. "To protect you. The rune would block the traits and memories, even the Parabatai marks you both had, but more importantly would disguise you."

"But you and Mom..."

"As adults we had some options that wouldn't have worked for you...and the rune allowed for us to stay together as a family."

"You know the rest." Magnus finished, "The Clave was thrown out of power...and there was a lot of...restructuring. But no solution can please everyone. Valentine had still been killed, Jocelyn and Luke had escaped, and there were members of Circle who were still angry. They pretended to assimilate to the changing world, but every once in a while a sleeper cell will make an appearance..."

"Like my parents?" Jace asked, connecting the dots.

Magnus nodded.

Izzy placed a supportive hand on her brother's shoulder. "Why now?"

"Clary is eighteen. The blocking rune has lost its power and I suspect her appearance at the club may have been spotted..."

"So if I wouldn't have followed Jace into the club..."

Luke cut her head off with a fervent head shake. He filing moved away from the window and moved closer to the trio who had been his patient audience, "Something else would have happened. There are a lot of points throughout the years, and a lot of decisions that have led us here. The only thing we can do right now is move forward. We will find Mom and we will get trough this..."

The werewolf turned to Simon, "Simon, you have been, in mine and Jocelyn's eyes a member of this family since we've met you, but this isn't your world or your fight..."

The young man interrupted, "You're a werewolf, these two" His thumbs gesture roughly toward Alec and Clary, "Are half-angel. And downstairs there's a warlock. And there's a bunch of angry bigots who want revenge. I'm not going anywhere." He ended with a wide grin, that was slightly forced despite his genuine intentions. Internally, he squashed the little voice of terror who wanted to run, because if this was really how the world was he was probably going to be safest under the protection of a werewolf and two half-angels. Right? He asking as he convinced himself. Of course right.

I know a lot of technical right? Its sort of my favorite challenge to write things that characters need to learn but the audience already knows all the details. I hope I did it justice, this really played in my brain like the tv show does. Although I have not read the books, its probably best to assume any above infromation that is non canonically correct is most likely due to it needing to fit within the context of this story's world.

I've also decided I probably should look for a beta, someone who not only knows the world tv and books, but can read for clarity and who would be willing to help me talk out ideas when I struggle with decisions. The outline and some the drafts for future chapters for this story are starting to look too much like a choose-your-own-adventure-book

Also I've posted this on AO3 under my penname: koserrainbow. Always I would love to hear thoughts, questions, and suggestions.

You may have noticed somethings didn't get covered above, there's a small percent that its because I didn't get to that portion yet and it will be in the next chapter, and that was intentionally left out by the characters and that info and those reason will be covered later on.

Coming Soon: what was supposed to be the rest of this chapter, everything else I promised at the end of the last chapter plus we get to see how Hodge fits in to the story. You guys will love it: and by love it I may or may not mean you will hate me for a little a while but in the end you will ultimately love it. Or at least that is the goal.

Thank you again for your patience and thank you for reading.