Chapter 2:

As promised, to all the lovely people that reviewed and asked for it, I delivered.

Note: I forgot a lot of City of Glass but I think this is pretty spot on, with some nice new parts added in. Anyway on with the story!

It was quiet in the Institute, no one brought up Valentine's name, once. Now everyone had left for Idris and were going to be staying with the Penthollows and Aline's cousin Sebastian Verlac.

"Hey guys!" Aline greeted hugging each Lightwood tightly.

"Hey Aline." Alec said with a smile.

"Oh right, did you hear? Imogen Herondale, the inquisitor was just fired, apparently they thought her decision to send Alec and Jace to Valentine were too extreme, she was even kicked out of the Herondale house because of it." Aline said lowly.

Alec frowned at her words and looked down.

"At least she was kicked out." Isabelle said putting a hand on her brother's back.

Aline looked awkward. "Sorry." She said with a blush.

Alec shook his head. "It's fine." Alec said smiling fakely at her.

"Right, anyway let me show you to your rooms." Aline said heading up the stairs.

Everyone followed and stopped as Aline stopped at a closed wooden door. "Isabelle and Clary will be staying in here." Aline said opening the door.

Isabelle and Clary nodded and entered the room, closing the door once they were in.

Aline headed up another set of stairs with Alec and Jace following.

"And this is where you two will be sleeping." Aline said as they entered the attic room.

"Oh, the attic, how appropriate." Jace muttered once Aline had left.

"At least it has a bathroom." Alec said opening a door that had a toilet, sink, and shower.

"That's something at least." Jace said laying on one of the beds before looking up at Alec. "Hey, are you okay? I mean Maryse told us some pretty shocking news." Jace said.

Alec turned and glared at Jace. "Am I okay?! I found out my mom cheated on my dad with Valentine! Freaking, I found out we're brothers and I…" Alec said and took a deep breath. "No Jace, I'm not okay." Alec said sitting down on the other bed.

"I guess now you know that you not in love with me." Jace said once a minute of silence passed through them.

"What?" Alec asked softly.

"I mean, no offense but you made it pretty obvious, dude. And I'm not judging I mean you're gay and thought you loved me, that's fine, at least now that's over with." Jace said throwing his arms up.

Alec looked mortified. "How…long have you…?" Alec asked his voice small.

"Known that you were gay? Or known that you liked me?" Jace asked Looking at Alec.

"Both I guess." Alec said with a shrug.

"I guessed on you liking guys when we were at Magnus's party, when he called you cute it was pretty obvious you like him. As for you liking me, I kind of always knew, I mean you would always look at me, act embarrassed if I changed in front in front of you, stuff like that." Jace said with a shrug.

Alec blushed and looked down. "Oh." Alec said.

"But now that that has been cleared, let's go get something to eat." Jace said getting off the bed he had been laying in.

"But…I still love you…" Alec said in a tiny voice.

"Yeah and I love you too, we're Parabatai Alec, and brothers." Jace said walking over to Alec's bed.

"No, I mean…mom said it herself, she isn't sure Valentine is my real father and I…" Alec said squirming in his bed.

Jace sighed. "If you really think you love me, prove it, kiss me." Jace said crossing his arms over his chest.

"What?" Alec asked blushing.

Jace exhaled and bent down grabbing Alec's face in his hands. Alec looked up at him with large terrified blue eyes. "I've already kissed my sister; I'm not above kissing my brother too." Jace said and pressed their lips together.

Alec sat frozen as Jace's lips collided with his. Once his body recovered he pushed Jace off of him looking at the blond in shock and horror.

"See? You're not in love with me." Jace said.

Alec looked hurt and angry and confused all at the same time, he wiped his mouth and ran into the bathroom slamming the door shut and locking it.

Jace sighed and walked down the stairs, not knowing that someone was sneaking into the room.

Alec looked at the mirror and glared at it, he was angry that Jace had kissed him, and sad that he spent years thinking he was in love with him. He splashed cold water in his face and walked out of the bathroom spotting a boy a little older than him sitting on his bed.

"Hello Alexander, I don't believe we've met yet, my name is Sebastian." The boy said smiling at Alec.

"Hi, and it's Alec, only my parents and the adults call me by my full name." Alec said shaking the boy's hand.

"Well, I am 19, I think that qualifies as being an adult, and besides, it's formal, and I like things to be formal. So tell me, Alexander, do you really believe that your mother would suddenly not know who your father is?" Sebastian asked.

Alec frowned. "How do you know about that?" Alec asked looking wary at Sebastian.

"A little birdie told me." Sebastian said grinning at Alec.

Alec glared at him. "Was that little birdie named Jace?" Alec asked.

Sebastian grinned but shook his head. "No, no. now there's no need to hate your Parabatai." Sebastian said and stood up, walking past Alec slowly. "Your father was never Robert Lightwood." Sebastian said lowly before he left the room.

Alec stood frozen, his mouth hung open as he stared at the space Sebastian had been in. "Then that would make…oh crap." Alec said and ran back into the bathroom, ready to empty out his stomach into the toilet.

Later that evening Alec finally went down the stairs, everyone was eating dinner when he came to the table and sat next to Isabelle. "There you are, Sebastian said he tried getting you, but you were in the bathroom apparently, you okay?" Isabelle asked handing Alec a buttered roll.

"Yeah, and I'm fine, sorry." Alec said taking a bite of the roll, he saw Sebastian look at him from the corner of his eye and ignored it, deciding it was better to leave it alone until he could talk to Isabelle alone.

Isabelle smiled started talking to him while Alec ate the roll, his stomach was too upset to take anything else and the stew his mother made was not helping.

"Hey, Iz. I'm going to go out for a while, cover for me?" Alec asked once dinner was over.

"Sure." Isabelle said with a nod.

Alec smiled and left the manor, hoping to get some fresh air and maybe see Magnus.

Magnus was easy to spot with his glittery bright blue jacket, his tight leather pants that seemed to be as shiny as the jacket, and spiked hair. Alec smiled at Magnus and walked over to him. "Hey." Alec greeted.

"Alexander. I do not like hiding in the shadows." Magnus said crossing his arms over his chest looking annoyed at Alec.

"I know, and I'm really, really sorry." Alec whispered grabbing Magnus's hands.

"Sorry? Tell me, why are you really hiding? To avoid your parents' disapproval, or Jace's?" Magnus asked glaring at Alec.

Alec jolted and looked down, not just because Magnus was angry at him, but after Jace had kissed him in their bedroom, he couldn't even look at Jace or hear his name without thinking of the kiss. "How'd about this, if we live through this war, I'll introduce you to my family, my parents included." Alec said.

Magnus beamed and kissed Alec deeply. "I say we have a deal, Alexander." Magnus said with a smile.

Alec smiled back and kissed Magnus before moving away from his boyfriend. "I'll see you." Alec said and left heading back to the Penhollow manor.

He was close to the building when he saw a shadow appear next to a dark space near nothing. Alec pulled out the only weapon he had on him at the moment- a dagger, and headed toward the shadow. "My son." Valentine said stepping into the light a smirk set on his face.

Alec glared and held his dagger up wanting to stab the evil man.

"You won't kill me." Valentine said laughing.

Alec glared and moved closer holding the blade closer to Valentine's neck.

"Why are you here?" Alec asked.

"We're family, is it weird to want to see your own son before the big battle?" Valentine asked unfazed by the knife pointed at his throat.

"You have a pretty awful version of family though. So yes, it is really weird, for you that is." Alec said.

Valentine smirked. "Meet me by the lake the day of the battle and all will be explained." Valentine said and disappeared into the shadows.

Alec looked around and had never felt more frustrated then at this moment. He sighed and put his dagger up, feeling suddenly tired.

Once he got inside he went straight up to his room and laid down hoping desperately to forget everything that had happened inside the manor. He closed his eyes and cracked them open as the door opened, looking to see who it was. It was Jace.

Alec frowned and turned over, making it seem like he was asleep. He heard the bed next to his creak as Jace sat down.

"Look man, I'm sorry. I acted out and did something I shouldn't have, it was wrong of me but I was just trying to prove a point." Jace said.

Alec sighed and looked up. "It was really stupid, but I guess I can forgive you this time, though if you do something stupid again I'll be a little less forgiving." Alec said and looked at Jace's left hand; it was covered in glass and blood.

"About that… see I was mad that you were mad, and then I saw Clary and that me feel worse so I smashed my hand through a window." Jace said causing Alec to sigh and sit up, turning the light on so he could look at Jace's hand.

"By the angel- Jace! What the hell!" Alec yelled before he rubbed his temples and grabbed a first aid kit.

"I knew you'd help me." Jace said with a smile. Alec glared and left the room, coming back with a bowl of water.

"Hold still moron." Alec ordered and pulled out a pair of tweezers from the first aid kit. Alec worked on getting all the glass out and grabbed bandages, wrapping Jace's hand up.

"Why not use a stele?" Jace asked. Alec glared and put up the first aid kit and went into the bathroom.

"Because, if you're going to act stupid like a mundane, you're going to heal like one." Alec said once he came back with the bowl empty and cleaned. Jace looked at his hand and sighed, he had a feeling Alec was teaching him a lesson some how, and that he was also getting back at him for kissing him.

Alec left the room again and came back a few minutes later empty handed. Once he entered the room, Alec looked at his bed and fell asleep in seconds, not caring that the light was on or that Jace was still sitting on the bed next to his, he was emotionally and physically drained.

The next day Alec felt better, he changed and got out of the room, he heard that all active Shadowhunters and Downworlders were to meet in the Hall of the Accords. He headed in and saw Clary explain that everyone was to find a Downworlder partner and draw a special rune on their hand. Alec smiled internally; he already knew who his partner was going to be.

Once everyone broke off, Alec took out his stele and drew a quick Fearless rune on his arm before heading over to Magnus. Magnus smiled at him while Alec worked on drawing the rune as painlessly as possible.

Once the rune was drawn, Alec looked up at Magnus, and thanks to the Fearless rune on his arm; he leaned up and kissed Magnus, not caring who saw, though he could feel everyone boring holes into him through their eyes. They had been kissing for a good couple of minutes until someone cleared their throat loudly.

Alec broke away, his cheeks bright red as he turned to see everyone staring at him. If he hadn't had the Fearless rune, he knew he would have cowered, but now he felt stronger and less afraid, though he didn't want to think about what was going to happen once his rune faded.

Alec opened his mouth only to close it again, unable to think of an excuse or a reason for kissing Magnus in the Accords Hall in front of everyone. "I'm uh, going to wait over there." Alec said pointing to the other side of the room.

"Good idea." Robert said with a slight nod.

Magnus smiled awkwardly and followed Alec, while the group of Shadowhunters began to murmur amongst themselves.

The rune had faded and now Alec was pacing with Magnus, Isabelle and Jace watching. "My life as a Shadowhunter is over." Alec said while he paced.

Jace sighed and stood up, grabbing Alec and stopping him from pacing any more. "First off, shut up. Second, you're being a bit dramatic." Jace said.

"Am I? You saw how they all looked at me." Alec said.

"Then why'd you do it?" Isabelle asked.

"I don't know! I mean I had a Fearless rune on, but…ah why did I put that stupid rune on!" Alec said sitting on a nearby bench and putting his head in his hand.

"Because putting the rune on and kissing me was the easiest way to come out to your parents?" Magnus suggested.

"Maybe, I don't know!" Alec said into his hands.

Everyone looked up as Maryse and Robert walked into the room. "We need to speak to Alexander privately." Robert said.

Alec gulped and looked at his friends helplessly, as they left before looking at his parents. "Yes?" Alec asked in a small barely audible voice.

"You're not in trouble, sweetie. We're just curious," Maryse said sitting next to her son.

"What made you gay?" Robert asked crossing his arms over his chest, he was standing over Alec.

Alec blinked. "What made me gay?" he repeated wondering if he heard that right.

"Yes, was it something we did? Is this just a phase you're going through?" Robert asked.

Alec blinked again. "Something you did?" Alec asked.

"Yes, was our parenting too soft on you?" Robert asked.

"No?"

Robert sighed in relief. "Well then did you eat something wrong, hit your head or something?" Robert asked.

Alec's jaw dropped. "No and No?"

"Well then this must be a phase you're going through, right? You'll be over this soon." Robert said looking relieved.

Alec blinked as Robert and Maryse left. "What?" he said in disbelief.

Everyone went back to their manors and got ready for the big battle. Alec put on his gear and turned to Jace who was also wearing gear. "Need me to apply any runes?" Jace asked.

Alec shook his head as he fastened his weapon's belt. "I'm good." Alec said and strapped his quiver over his chest.

Jace nodded. "Well then help me out. I need an agility and swiftness rune." Jace said handing Alec a stele. Alec nodded and carefully applied the two runes. That was one thing Jace liked about Alec, his runes were always careful, accurate, and had a nice flourish to them.

Once Alec was done he handed the stele back to Jace and grabbed his bow. "See you after the battle." Jace said giving Alec a quick good luck hug before putting a couple Seraph blades on his belt and heading down the stairs. Alec followed shortly after and stopped as he looked at Isabelle and Max.

"You two going to be okay?" Alec asked.

"Yeah, I want to go with, but someone has to watch Max, you just be safe." Isabelle said hugging her brother.

Alec nodded and glanced at Sebastian who was sitting on the couch reading a book. "Stay safe." Alec said to his younger siblings. They both nodded and waved as Alec left.

The battle had started, Alec shot down demon after demon. When suddenly, he froze. The battle was going on around him but he didn't notice, he felt like a part of him had died, like there was an invisible tether and that tether had broke and now he was falling.

"Wither thou goest, I will go." The words were swimming in his head. He dropped to the ground and felt like everything was going in slow motion. He gripped his Parabatai rune tightly and felt like it was bleeding.

Magnus was by his side and watched as the rune began to run, turning Alec's hand black. A demon had charged toward the stunned Shadowhunter, but Alec couldn't move, he was glued to the spot. Magnus swore and shot down the demon, looking to his boyfriend while keeping an eye on the battle.

And then Alec stood up, his rune was still bleeding, but he was walking to the lake, stumbling and gripping his rune tightly while Magnus followed, worried about his boyfriend.

Alec had made it to the lake, but after he got there and saw a large angel standing over Valentine, he felt his eyes roll back; his body fell back into Magnus's arms as he fainted.

When Alec awoke, he was in the infirmary of the Accords hall with Silent Brothers looking over him staring at his Parabatai rune. Though Alec had protested saying he was fine. "I told you, I'm fine." Alec said, though the Silent Brothers disagreed.

After two days of staying with the Brothers with them asking him things like 'What happened' or 'Do you still feel faint' 'Did you feel something was wrong with your Parabatai', Alec was finally permitted to leave.

Alec sighed and went back to the Penhollow manor, where his family stood crying. Alec saw Jace among them and let out a sigh of relief before he went over to them. "What happened?" Alec asked.

Isabelle sobbed. "It's Sebastian, he-he killed Max!" Isabelle said in between sobs.

Alec paled. "What?! What happened?" Alec asked.

"Sebastian, he hit both of us in the head, but it just knocked me out. Max though, Max died." Isabelle said her sobbing uncontrollable.

Alec swallowed heavily, he had always had a bad feeling about Sebastian, and yet he left his younger siblings stay with him. "I left you two alone with him, I had a bad feeling about him, but I left you with him anyway, it's my fault…" Alec said softly, his eyes tearing up as he thought about Sebastian killing his little brother.

"There's nothing you could have done differently, Alexander. You were needed on the battlefield." Robert said.

"Yeah, and its Sebastian Verlac's fault, not yours." Jace said.

"His name isn't Sebastian Verlac. It's Jonathon Morgenstern. He told me that before knocking me out." Isabelle said, she had stopped crying, but now she looked angry.

"But that's Jace's name, there can't seriously be two Jonathon Morgensterns, can there?" Alec asked.

"Your right, there aren't two Jonathon Morgensterns, but there is one, Sebastian." Imogen Herondale said walking over to them.

"But if Jace isn't Jonathon Morgenstern, who is he?" Isabelle asked.

"He's Jace Lightwood of course." Maryse said. Jace stared at the ex-Inquisitor in shock.

"So, I'm not related to Clary?" he asked looking giddy.

"No. your not." Imogen said with a small smile. Jace smiled and looked ready to kiss the woman before he ran off, most likely to tell Clary the news.

Alec unconsciously reached for his Parabatai rune; the Silent Brothers had covered it, mostly because they had never experienced something like this before, never before had they seen a Parabatai rune completely bleed out and then go back to being black.

"Oh right, what happened to Sebastian?" Alec asked turning his attention back to his family.

"He's long gone. He probably left after his father died." Maryse said.

"Oh." Alec said looking down.

"Yeah I know, I wanted to kill him too, but if we ever see him again, we'll tag team and kill him together." Isabelle said smiling at her brother.

Alec smiled back, though that wasn't why he was upset. He wanted to know what Sebastian knew; he wanted to know if Valentine was truly his father, or if Valentine had said that to mess with him.

"You know we just won a war and Valentine's dead, let's get everyone together and celebrate." Magnus said trying to lighten the mood.

Everyone said yes. The party was a day after Max's Pyre.

While Alec had watched the fires he felt a rage build in his heart. He was going to find Sebastian Morgenstern and question him before killing him.

So? Chapter 2 is done! Review if you liked it or if you found you're self asking WTF, that's fine two, I just like the reviews. If you continue to like I'll do a Chapter 3.