Disclaimer: I do not own these characters. They belong to Cassandra Clare and I wouldn't have it any other way!

Summary: The New York Institute has been compromised, and Sebastian and Valentine are in the wind. The High Inquisitor is out for blood, and her wrath has zeroed-in on the current head of the Institute; Alexander Lightwood. She decides to make an example out of him, but will her punishment take things too far?

Hurt!Alec and Protective!Jace/Magnus/Izzy/Maryse. Takes place at the end of s02e18.

A/N: This chapter is dedicated to all of you wonderful readers who have stuck with me and left inspiring comments that have kept this story going till the very end. Thank you all for your support, and I hope the big finale was worth the wait!

The moment Alec stepped foot back in the Institute, he was descended on by a multitude of Shadowhunters, all of whom were desperate for his guidance.

He answered questions, gave orders, signed papers, and eventually made it to the safety of his own office, only to find a giant stack of neglected work sitting on his desk.

It was going to be a very long day.

Alec resignedly set to it, cursing Valentine even more for being such a monstrous thorn in his side.

Twenty-four hours… That's all he had missed. But thanks to the Circle leader's constant movement, there were enough reports to keep him busy for a month.

Hours of grueling toil passed before a knock on his door interrupted his thought process.

Oh well. He was pretty sure he had just read the same sentence ten times anyway, but his overtaxed brain was refusing to ingest the information.

Alec put his pen down and sighed heavily when he realized that his to-do pile was still five times higher than his addressed one. Maybe a quick break wasn't such a bad idea.

He checked his watch and was surprised by how much time had already passed. It was a little after 2pm and he had missed lunch. No wonder he was having trouble focusing…

"Enter," he called out, then inwardly groaned when his sister came storming into the room. He knew she would find him eventually.

"Underhill just told me you were in your office, but I told him that couldn't be true because you were taking a well-deserved day off. And yet, here you are!"

That tone and that pose, with her hands on her hips, were definitely inherited from their mother.

"Hello to you too," he replied dryly.

"Seriously, Alec… You should still be resting. Jace and I can…"

"I'm fine, Izzy. Most of the damage healed shortly after the Agony rune was removed. I can handle a few aches and bruises. So if you're only here to berate me for not slacking off, then I'm going to get back to work."

Attempting to dismiss her, he picked his pen up again and signed a few more documents that were waiting for his stamp of approval.

Izzy didn't take the hint though. She studied him for a moment, choosing to make her own assessment of his wellbeing rather than accept him at his word.

"You do seem less pale…" she admitted reluctantly as she approached, rounding the desk and sitting down on top of it, clearly not intending to leave anytime soon. "But it's not the physical damage that worries me."

Alec dropped his pen a second time with an exaggerated eye-roll and sat back in his chair, arms crossed defensively to put more space between himself and Isabelle.

"And what's that supposed to mean?"

"I'm not an idiot, you know. Something really bad obviously happened to you, and no one is talking about it."

"Good. It's nobody else's business," Alec grumbled.

"I get that. But if you ever decide that you want to talk about it… I'm here for you, big brother. Forever and always."

Alec forced himself to relax and let his walls down a bit. Izzy was right. She had always been a good listener when he needed to vent, and none of this was her fault. He shouldn't take it out on her with his snippy attitude.

"I know you are, Izzy. And thanks."

He dropped his arms to fiddle with his hands in his lap, avoiding eye contact as he considered her offer.

"I guess there is one thing I could use your advice on…" he finally admitted.

"I'm all ears."

After a moment, he glanced up at his sister through his bangs.

"I'm worried that what happened is going to affect my relationship with Magnus."

"How so?"

"He uh… He kissed me this morning, and I pulled back. I didn't mean to though. This image just flashed through my head and took me by surprise."

"You've been through a trauma, Alec. It's going to take time for those types of wounds to heal."

"But everything was fine last night!" he ranted in frustration.

"That may be true, but you were also barely conscious last night," she pointed out. "That's not really a valid comparison."

"Fair enough, but I kissed him again shortly after. No flashbacks or issues the second time. It's completely random and doesn't make any sense!"

"Triggers can be unpredictable, big brother. Don't beat yourself up for something you can't control. It'll get easier, and if you need to take things slow again for a while, I'm sure Magnus would understand."

"I know he would. But somehow, that just makes it even worse." Alec dropped his head into his hands and tried not to cringe when Izzy's hand landed on his shoulder.

"You still love him, right?"

"Of course I do," Alec muttered miserably.

"And he obviously still loves you. That's all that really matters. The rest will work itself out. Make sure you don't push yourself too far, or too fast. Wait until you're ready."

"I should've just let Raphael Encanto me. Then maybe things would've gone back to the way they were before."

"Alec, look at me," Izzy instructed, then waited for her brother to wearily lift his head. "Burying the past doesn't make it go away. You made the right decision in facing it head-on.

"It's not going to be easy, but you've got a pretty awesome support system this time around, so don't feel like you have to face it all on your own. We've got your back. Whatever you need."

The sincerity in her eyes made Alec's heart ache, so he stood up and pulled his sister into a gentle hug. She nestled into his chest and rubbed his back until the ache dissipated enough for him to breathe again.

Alec closed his eyes in relief and held Izzy tighter, feeling like a weight was being lifted higher off his shoulders with every passing second. The internal pain was mending.

"Thank you," he whispered against her ebony hair before pressing a tender kiss to her forehead.

A brief knock on the door interrupted their moment mere seconds before the newcomer came bustling in without an invitation, clearly not expecting anyone to be in the office.

Alec reluctantly pulled back from his sister, donning his Head of the Institute cap and hoping like hell that he didn't look like he was on the verge of tears as he turned to address his visitor.

It was Maryse. Alec blinked at her in surprise.

"Mother?"

She came to an abrupt halt when she saw her son.

"Alec…? What are you doing here? Jace told me you left with Magnus."

"I did, but I came back a few hours ago to get some work done. Why are you still here though?" he volleyed back in confusion. "I thought you would've left for Idris by now."

She held up the stack of file folders which she had carried in with her.

"Just doing my part to try and lighten the load a bit until you're back on your feet."

Alec glanced at his already buried desk and grimaced. "About that… I know I've fallen behind a bit, but I swear I will get this Institute back on track as soon as I…"

"Oh, hush. I don't care about any of that." She walked right up to him, dumped the folders on the desk, then gripped his biceps, turning him to face her directly. "Let me get a good look at you. How are you feeling? You really shouldn't be pushing yourself like this…"

Alec shifted uncomfortably from the surplus of attention that he wasn't used to getting. Before he could reply, Izzy interrupted.

"I told him to take some time off, but he didn't listen to me," she announced, holding back a giggle as Alec sent her a death-glare over Maryse's shoulder.

"I'm fine, Mom," he insisted, turning his attention back to the older woman. "Really."

Maryse smiled proudly at him. "Of course you are. You're a Lightwood, after all."

Alec subconsciously stood taller at the reminder, then winced as the movement pulled on the abused muscles in his back. Maryse gave him a sympathetic look as she ran her hands soothingly up and down his arms.

"But that doesn't make you invincible, sweetheart. If you need more time to recover, then you should take it. In fact, why don't you head back to Magnus's now and get some proper rest? I'll finish the paperwork for today before I head out."

"Head out?" Izzy questioned, sounding disappointed. "When?"

"Tonight," Maryse lamented. "I had hoped to stay longer, but unfortunately, new orders have already been passed down. I just told Max to pack his things so I can send him to Alicante where your father can keep an eye on him until this Valentine business is over."

"A-Alicante?" Alec stuttered, a cold dread spreading through his insides. He froze as memories assaulted his mind again.

Alicante. The demon towers. A shadowy figure climbing over one. Smoke, fire. Izzy stumbling in disorientation, and Max…

There was blood. Lots of blood.

Max wasn't moving.

"It should've been you," Robert stated plainly, disappointment in his tone and face. "You let this family down again, Alec. And now your little brother is dead, and it's all your fault."

"Alec? Alec! Are you alright?"

Alec snapped back to the present to find his mother watching him worriedly.

"Max stays here," he forced out through a clenched throat.

"What? Why?" Maryse pressed, her concern increasing by the second.

"Alicante isn't safe. I can't explain why, but I need you to trust me. Max has to stay here. With us."

"Are you sure it's wise to keep him in the Institute? Jonathan has been in this building countless times…"

"And he's not stupid enough to come back now that his cover has been blown. He wouldn't make it within twenty feet of the place."

"But, Alec…"

He took his mother's hand into his own.

"Mom, please. Promise me."

Maryse could read the desperation in his eyes, and she nodded. "Alright. Max stays here."

"Thank you," Alec rasped.

He let out a breath he didn't even realize he was holding as dizziness overwhelmed him. He suddenly felt unbalanced and weak on his feet.

Maryse saw him starting to falter and quickly eased him back into his chair.

She leaned down and cupped his cheek to help steady him as he fought his way back from the disorientation.

She frowned at the heat coming off his skin and slid her hand up to check his forehead.

"You still have a bit of a fever…"

"It's not that bad," Alec protested. "Just got a little lightheaded is all."

"Nice try. I think you've had enough for one day. Wrap up what you were working on, then go."

"That's not necessary, Mother. Really. I'm…"

"Don't make me call Magnus to come and get you."

There it was- the hands on the hips.

With the exhaustion creeping up on him again, Alec didn't have enough energy to put up a real fight. Plus, now that he was actually entertaining the idea, going home to Magnus was exactly what he wanted to do.

"Okay," he relented. "I only have a few more memos to get through, so I'll finish those up and take off after that."

"Good choice. Don't dawdle now. I'll go tell Max to unpack, and when I return, I want you ready to leave, understood?"

"Yes, ma'am."

She kissed him on the cheek before straightening up and turning to her daughter. "Isabelle, why don't you go track down Jace and let him know Alec is alright. He's been terrorizing the foot soldiers all morning."

This time, it was Izzy's turn to roll her eyes. "Sounds like Jace…"

Alec winced. He probably should've sought out his brother when he first arrived, but Jace was handling a meeting in the Ops Center on his behalf and Alec wasn't prepared to interrupt and get hounded by questions he didn't want to answer.

So instead, he had slipped past, unnoticed by the blond, with every intention of finding him later when things had quieted down a bit. But by then, time had gotten away from him.

Jace was definitely going to kick his ass in sparring at some point for ducking him.

Izzy moved closer and rubbed Alec's back for a moment. "Feel better, big brother. And keep us posted."

"I will."

After Izzy and Maryse left the room together, Alec rolled his chair forward to finish with the small stack of memos he had set aside for himself. He was signing the last one when another knock came at the door.

Seriously?

This time, he groaned out loud, massaging his temples with the thumb and middle finger of his left hand as he tapped the end of his pen against the desktop, praying to the Angel for patience.

He had been so close to going home.

For a brief moment, he assumed it might be Jace, coming to add his two cents to the mix. But Jace wouldn't have bothered to knock. He would've just barged in.

Maybe Underhill then, apologizing for squealing on him to Isabelle…

"Enter," he directed, then glanced up as the door creaked open.

The hair on the back of his neck rose when he saw who it was. He stood at attention, his hands clenching into fists by his sides as he greeted the short but mighty woman brusquely.

"Madame Inquisitor…"

"At ease, Mr. Lightwood."

Imogen came to a stop in front of his desk, noticing how tense he became the closer she got. She could hardly blame him, given recent events.

"Relax. I mean you no harm," she stated. "In fact, I've come with happy tidings for you. I've decided to resign as High Inquisitor."

Alec felt like someone had slapped him with a dead fish.

"You… You're stepping down? Why?"

"It's quite simple, really. I figure it's only a matter of time before the Clave hears about the unfortunate incident with the Agony rune. I intend to leave my position before that day comes, and with my good name still intact, if you'll permit it."

She wasn't just quitting then. She was running away. Because of him. And her reputation was his to destroy, should he choose to inform the Clave of her misdeeds.

Suddenly, the prideful woman didn't seem quite so intimidating to Alec.

"…I'm not sure what to say."

"You don't need to say anything. I've already made my decision, and I believe it's for the best."

"Who will be taking over?"

"I suspect the young upstart, Victor Aldertree. He already has a lot of support from the Council, and I have no doubts that he'll perform admirably in my stead."

Alec knew nothing about this Aldertree guy; whether he'd be an asset or a liability when it came to his plans for reuniting the Shadow World. At least with Imogen, he knew where they stood.

And now, he might be able to use that to his advantage.

"Do I have any say in the matter?" he inquired, carefully keeping his voice void of emotion.

"The final decision will be up to the Council, but I'm sure Mr. Aldertree will be properly vetted before he's given command."

"I'm not talking about him. I'm talking about you stepping down."

Imogen's eyebrows drew together in perplexity.

"I'm afraid I don't follow…"

Alec drew in a steadying breath, then rounded his desk to face the woman directly.

"In short, I don't think you should resign."

The Inquisitor was taken aback. "I have to admit, that's the last thing I expected you to say."

"We're on the brink of war," Alec stated bluntly. "These are desperate times, and thanks to Valentine, our people are splitting into factions. I need to know that there are still members of the Clave that I can trust."

"And you're saying you trust me?" Imogen asked skeptically.

"Not particularly," Alec admitted. "But you owe me now. Consider this your chance to repay that debt."

"So this is blackmail then," she huffed. "I should've expected as much from a Lightwood."

"No," Alec practically growled. "I am not my father. This is simply my attempt to build an alliance."

Imogen studied him, intrigued. "Explain."

"The way we run things is no longer working. We have to adapt to survive. Unfortunately, many Shadowhunters are set in their ways, and they'll need some convincing first. I can't do it alone. I don't have enough pull. But you do."

The woman actually looked impressed. "How very political of you."

"My offer is this; You keep your position, and when the time comes to vote on restructuring, you help me gain support. And in return, no one else will ever hear about yesterday's events."

Imogen nodded thoughtfully, then glanced back towards the closed door. Unless Alec was very much mistaken, she actually seemed afraid.

"I'm not sure my grandson will approve of our working together."

"Let me handle Jace. But if this is going to work, then there's one more thing I need from you. Swear to me that you will never ever use that Agony rune on anyone else. Not even to interrogate Circle members."

Imogen dropped her gaze in shame.

"After seeing the effects of my rune firsthand, you can rest assured that I will not be making that mistake again. My first order of business will be to abolish its use in the Clave."

"Then I'd say we're already making progress."

When she looked back up at him, there was a newfound respect in her eyes.

"It seems that I've underestimated you, Mr. Lightwood. A mistake I have no intentions of making again. You were clearly born for this job, and I expect to see great things from you."

"And I will do my best not to disappoint. Do we have an accord?" Alec stuck out his hand, and Imogen shook it. "Then I believe our business here is complete."

Alec moved to pull away but stopped dead when the woman caught his forearm.

"Before I go, there's something else I need to say. Had I been aware of how unstable that rune was, or of the traumas you faced in the past, I never would've used such a punishment against you. I don't know if it even matters at this point, but I am truly sorry for what I did."

Alec gave her a curt nod.

"It matters. Thank you."

Imogen bowed her head respectfully. "Good day, Mr. Lightwood."

She turned and left him to his thoughts again.

The longer he stood there on the far side of his buried desk, the more his skin began to itch and his need to leave grew. The only thing he could think about was getting back home to Magnus.

The second Maryse returned to relieve him of duty, Alec was out the door and headed down the hall towards the exit. He hit the button for the elevator and waited impatiently for it to arrive.

"Were you seriously just going to leave again without saying goodbye?" came a voice from his right.

Shit. Jace…

Alec turned to find his brother leaning casually against the wall, arms crossed and looking expectant.

"Sorry, Jace. It's just… It's been a really long day, and…"

"And you want to go home," the blond finished for him, making Alec wince at the bluntness of it.

"The Institute is still home for me too," he quickly reassured. "But given everything that's happened, I just need some time away."

"I get it, Alec. Seriously, I do. But let's be honest. This place never really felt like home to you."

There was no getting anything past his Parabatai. Alec sighed in defeat.

"Jace, I…"

"You don't need to explain. It makes perfect sense. This place is your job, and as long as you're here, you feel like you can never let your guard down. Never be yourself. You're working 24/7, and that's enough to drive anyone mental. I'm glad you finally found a place to call home."

"It's only temporary," Alec replied. "I'll be back in a few days. A week, max…"

Jace shrugged.

"Why though? We'll always be here, Alec. Whenever you need us. But there's nothing wrong with getting a life of your own. And no rule saying the Head of the Institute has to live on site."

Alec's eyes narrowed in puzzlement.

"Why are you saying this?"

"Because you're happier at Magnus's place. So maybe you should consider moving in with him. On a more permanent basis."

The older boy snorted incredulously. "Are you serious? Jace, Magnus and I have never even discussed…"

"He's going to though. Spoiler alert… He asked my opinion last night while we were sparring. I think he figured you might need some convincing to leave the nest and hoped I'd tag in."

"And what did you say?"

"I told him if that's what you want, then that's what I want for you." Jace pushed off the wall and moved closer to his brother. "In all the years I've known you, Alec, I've never seen you smile the way you do when the warlock's around."

Alec smiled at the thought alone, proving Jace's point.

"You guys are good for each other. And I think a change of scenery could be good for you too.

Just uh… Don't be a stranger, alright?"

The naked fear of abandonment in the blond's eyes nearly brought Alec to tears again.

"Jace, we're Parabatai. Wherever I go, you're right there next to me. That's never going to change."

The younger boy beamed at him, then pulled him into a bone-crushing hug, which Alec happily returned.

"I love you, buddy," Jace stated.

"I love you too," Alec replied sincerely.

"Say hi to Magnus for me," the blond requested, then clapped his brother on the back before pulling away. "And don't do anything I wouldn't do."

He winked and Alec shook his head in amusement.

"There's nothing you wouldn't do, Jace."

"Damn right. So go have some fun."

That was exactly what Alec intended to do.

SHSHSHSHSH

By the time he made it home, Alec was a mess of emotions, spanning from guilt and sadness at the thought of leaving the Institute, to hope and elation at the promise of a future with Magnus.

Everything was changing so quickly around him, and he had gotten swept up in the whirlwind. But there was one constant in his life these days, and he had no intentions of letting him go again.

Magnus was in the kitchen preparing dinner when he heard his boyfriend enter.

"Alexander? You certainly made good time! I've barely started putting my ingredients together…"

"I left early," Alec replied, appearing in the doorway. "Couldn't wait any longer."

Magnus raised an eyebrow at him. "Wait for what?"

"For this."

Next thing the warlock knew, he was being pressed against the countertop, Alec's lips planted firmly against his, practically devouring him in his desperate need.

After a minute or two, the warlock eased him back slightly to see Alec's flushed face.

"Not that I'm complaining, darling, but what brought that on?" he asked with a curious grin. "I may need to reenact the events at some point."

"I spoke to Jace," Alec panted.

Magnus looked wary. "Interesting segue…"

"And the answer's yes," the Shadowhunter finished.

"Wonderful! Might I inquire as to the question?"

"I want to move in with you, Magnus. I want to make things official between us."

The warlock's smile grew exponentially at the declaration.

"Well that was easier than I anticipated… I had a whole speech planned and everything! But are you sure you're ready for such a big step, Alexander?"

"I'm positive. This is where I want to be. This is where I belong. With you."

"I couldn't agree more," Magnus beamed, earning another gratifying kiss.

"It smells fantastic in here, by the way," Alec stated before pulling back to look at the organized chaos on their kitchen counter. "I'm starving."

Magnus's face fell as he caught sight of his array of lackluster ingredients again.

"What's wrong?" his boyfriend asked, sounding worried.

"Nothing. It's just… Had I known this was going to be such a momentous occasion, I would've prepared something a bit more special than a stir fry for dinner," he lamented.

Alec shook his head with a grin. "It's perfect, Magnus. You're perfect." He kissed the warlock's cheek and was thrilled to find the contented smile back on his boyfriend's lips.

"Well in that case, I suggest we celebrate properly!" With a snap of his fingers, they each had a glass of red wine in hand. "To us," Magnus toasted, and the glasses clinked together.

Dinner passed pleasantly enough as they both discussed their day. Magnus wasn't thrilled to hear about Imogen's unexpected visit, but he agreed that Alec's compromise with her was for the best.

"You never cease to amaze me, Alexander."

And with full stomachs and light hearts, Alec felt his exhaustion creeping back up on him. He stifled a yawn with a quick apology, then Magnus magicked the dishes clean and suggested that they head to bed.

Alec was the first to enter their shared bedroom, and when his eyes landed on the large, ornate bed against the far wall, he couldn't help but freeze up for a moment.

Magnus, who was only a step behind him, placed a hand on his shoulder in concern. "Alexander? Are you alright?"

Alec jumped at the touch, swiveling his head around to lock eyes with the warlock.

"Yeah, sorry. I just…" He trailed off, at a complete loss for words. In truth, he didn't know why he reacted that way.

Was it thoughts of being strapped down to Camille's bed, which was similar in size and decor? Or was it the idea of having sex with Magnus again, now that he was officially moving in?

He wasn't sure he was ready to take that step quite yet.

"You don't have to explain," Magnus promised softly. "We don't need to rush into anything. We have all the time in the world now."

"I know," Alec muttered glumly, wishing he could just get past it all and be with Magnus the way he wanted to be. "Logically, I'm aware that it was all a long time ago, but it feels like it was just yesterday thanks to that damned rune."

"In some ways, it was," the warlock reasoned. "Those memories were repressed for years, and you never had time to properly confront them before. That would be a confusing situation for anyone."

"I guess. It's just… I keep trying to ignore it, but I can… I can still feel her hands on me," Alec admitted with a shiver of disgust.

"Perhaps I can help with that," his boyfriend offered.

He snapped the fingers of his free hand to bring some ambiance to life, including the warm glow of candles and the smell of lavender and sandalwood incense, chasing away the dark shadows that lurked in the corners of the room.

The boy tensed up further as he took in the romantic scene before him. He started shaking his head.

"Magnus, I don't think I can…"

"Shh… It's alright, darling. We're not having sex tonight."

Magnus knew he had made the right decision when some of the tension eased from his boyfriend's stiff back.

The warlock cautiously placed his free hand on Alec's left shoulder, mirroring the one on his right. His thumbs gently dug into the knotted muscles at the base of Alec's neck, taking care not to cause him any additional pain.

"Just relax, and stay here in the moment with me, Alexander. Feel my hands on your skin now. No one else's."

He leaned forward and placed a comforting kiss to the same spot on the boy's neck that he had just loosened, before sliding his thumbs down and out, drawing lazy circles across Alec's shoulder blades.

"Let me replace those memories with better ones," Magnus continued with a whisper next to Alec's ear. "Let me worship you, my love."

Alec let his tired eyes flutter closed as his breath shuddered out of him, and with it, his remaining anxiety. By the Angel were Magnus's hands magical…

The warlock shifted his palms down to Alec's ribs and guided the boy forward until his knees met the edge of the mattress. Then he drifted lower and tugged on the hem of the boy's shirt in question.

Alec didn't need any more encouraging from there. He raised his arms and allowed Magnus to remove the garment, then crawled wearily onto the bed. He settled into a comfortable position on his stomach, wrapping his arms around the pillow that he pulled under his head and chest.

Magnus knelt on the mattress beside him and picked right up where he had left off after summoning his massage oils.

He released every knotted muscle he could find as he glided his hands seamlessly up and down Alec's strong back and arms until the boy felt like he was floating weightlessly through clouds.

Alec's flesh was so warm now, heated by the kinetic energy of the warlock's ever-moving hands.

Magnus took his time, tracing every fading scar he could find on Alec's torso from top to bottom, then followed the path with his lips, kissing each mark gently until the boy moaned deeply in approval.

The warlock smirked against his skin.

"How're you doing, Alexander?" he inquired, rubbing soothing circles over the boy's upper back as he laid down next to him, watching his boyfriend's relaxed face.

Alec blinked his beautiful eyes open just far enough to see the blurry outline of the warlock beside him.

"I love you, Magnus," he whispered out, making Magnus's heart soar with delight and affection.

"I love you too," he stated in return, then waited until the boy's eyes fluttered shut again.

Alec was going to be okay. They both were. Because love conquers all.

Magnus reached out and gently brushed Alec's bangs to the side, smiling as his favorite little snores began to rumble from the boy's throat.

"Aku cinta kamu, my dearest Shadowhunter."

The End

A/N: That was quite a long ride! Thank you all for sticking with me, and I hope you enjoyed the story!