AN: Hey guys sorry for not updating for ages but I've been stupidly busy and also I have had loads of homework too and I've had to keep deleting loads of this work because it didn't work well or it didn't seem right. Anyway I'm sure all of you want to just read now so I'll let you guys do just that and I hope you all like it.

Jace's point of view

I glanced at Luke before jamming my key into the lock and pushing the door open I saw Izzy and Jessica backing away into the corridor.

I ran towards the door and I almost gasped in surprise.

There right in the centre of Clary's room stood her brother Jonathan Morgenstern and I scanned the room for Clary and I saw that she was lying on the floor next to a wall looking half unconscious.

Jonathan had a blade pointing at Clary and another pointing at us.

Luke stared at the young boy and asked uncertainly "Jonathan? Is that you?"

Jonathan laughed and said "Oh hello Lucian, I didn't think that you'd be here now. Getting a bit old aren't we?"

Clary groaned from the floor and her eyes flickered and she muttered something that sounded like "Ouch that hurt more than I was expecting.

Jonathan growled at her "Be quiet Clarissa, you know how father hated you to talk out of turn."

Clary blinked a few times and said "Yeah well father's a teeny bit dead now."

Jonathan looked angry and he snapped "Oh not for long dear sister you may have put a knife in his back but he will be raised soon."

Clary looked mildly confused before it obviously clicked and she told her brother "Jonathan, you can't do that, it is cursed for anyone who's tried."

Jonathan smiled at her but it wasn't a warm happy one it was a cruel and cold one.

He turned to us and he took all four of us in and he said "Oh look Clarissa you've made friends, not very like you there, you used to hate people really, always got on better with animals."

Clary snarled "You don't remember anything from our childhood together Jonathan, you only remember what the serum wants you to."

Jonathan yelled at her "THAT'S ENOUGH!"

Even Clary looked slightly scared as though it reminded her of her past again but she said "Leave here Jonathan, you have no business here."

Jonathan saw that Magnus, Ragnor and Alec had now joined the group at the door ad he told Clary "Looks like a few more have come to join in the audience now Clarissa."

Clary rolled her eyes and asked him "The bigger the better?"

Jonathan ignored her and then saw me standing among the others and he said "Ah if it isn't Jonathan Herondale, last time we met you tried to kill me to protect my darling little sister I believe."

I didn't answer him I just stared at him blankly like Clary used to do to me.

Jonathan smiled and said "One of my spies tell me that you can fight very well now so I might have to take you."

Clary said sternly "No Jonathan, leave them out of this."

Jonathan just laughed and then offered to me "Come with me Jonathan Herondale, come and finish what your parents died for."

Clary tried to protest but Jonathan grabbed her and threw her as in picked her up and threw her straight into the wall again which knocked her unconscious.

Jonathan sighed and muttered "Dammit, she always seems to go unconscious every time."

I wanted to scream at Clary and fight Jonathan myself but I heard Clary's words from earlier come back to me from when Jessica asked her if she was afraid of her father and brother her answer had been "I'm afraid of my father and brother because if you were smart enough you would fear them the most too. Dead or not."

I could see what she meant now from when I fought against him what felt like ages ago now I had almost been killed and I had felt something different about him which was also in Clary when she fought properly against bad people who she wants to injure or die, he doesn't care if he dies, or get badly injured he just wants to do something for the world whether it's good like Clary or bad like himself.

A flash then lit up behind Jonathan and he sighed before saying "Well it looks like we have to leave now, shall we meet up next week same time?"

Izzy asked him "What do you mean by 'we'?"

Jonathan laughed and then said "I mean me and Clarissa, raven haired girl and only me and Clarissa."

I watched frozen to the spot as Jonathan bent down and picked Clary's unconscious body up off the floor in a bridal style before saying to us "Goodbye my sister's friends and oh look there's the temporary director Scott oh and little rat friend too Simon wasn't it?"

Simon stepped next to me and said "Well done Sherlock and let Clary go or we'll fight against you Jonathan."

Jonathan looked at the red girl in his arms and said "Nah I'm good thanks."

And with that he stepped back through the flash which surrounded both of the siblings and then with a blinding flash both of them disappeared into empty air.

Simon seemed to almost deflate as soon as Clary was gone and I probably did something similar he said ever so softly that I think that only I heard him "A portal, one of Valentine's projects, she's screwed. Why didn't I do something to help her?"

Jessica turned to Agent Scott and screamed at him "Why did you just let him take her? She hates and fears him so why do you let him go and take my half-sister off into the middle of nowhere?"

Agent Scott told her gently "We lose soldiers everyday Miss Fairchild, we can't rescue every single one."

Jessica looked like she was going to thump the step in director but instead Luke grabbed her and said "Jess you need to calm down, Scott's right we lose people every day and they can't rescue all of them either."

Jessica looked back at the spot they disappeared at and she whispered "Why do you talk about her as if she's dead? She isn't, she can't be!"

Simon knelt down next to her and told Jessica "She's pretty much as bad as dead, living with her brother and if he's going to do what I think he is then it won't be long before her father is there too."

Jessica looked at Simon and she said "What are they going to do to raise him?"

Scott came up and agreed "Yes Agent Lewis, what are they going to do?"

Simon hesitated for a while as though debating to tell them or not.

Simon seemed to eventually agree with it so he said "It's an ancient trick, Clary spoke of it only once or twice to me after we left the manor."

Scott remained unimpressed as he encouraged "Continue please Mr Lewis."

Simon looked slightly uncomfortable as he tried to explain "I don't know much about them but from what Clary told me I can tell you most of it."

Scott scowled and snapped "Just get on with it Agent Lewis"

Luke then stood up for Simon which was almost surprising "Scott, you can't expect him to talk on command, he just saw his best friend disappear and he can almost guarantee that she is now in danger if she's not already dead."

Scott looked surprised and he said "Fine but I want to know as much as possible Agent Lewis and for you Mr Greymark I don't think that this is any of your or your daughters business now."

Luke snarled "It is if Jocelyn's daughter has just gone and got herself into danger again."

Scott looked into his eyes and asking "You really do care about Agent Fray don't you? Or is it the fact she looks so much like Jocelyn that you now want to date her too?"

Luke looked enraged but he just said "I owe Jocelyn a debt, if I have to pay it through Clary then I will."

Scott glared at Luke quickly before saying "Anyway Agent Lewis what was you saying about whatever they're going to do?"

Simon looked stranger now almost as if he'd grown older in a matter of a few minutes without Clary being here to make him smile or laugh.

Simon sighed and explained "Basically it is a very old as in ancient old piece of work. It is said that if a living man has betrayed his family and a faithful man is dead then if you kill the living man and feed the blood onto the bones or ashes of the dead man's remains then they will swap lives so the dead one would take the years left of the living one and the living one would die pretty painfully."

Scott asked him "Is this real or is it just a bluff?"

Simon shrugged and answered "No one alive knows, the very few people who have tried to do just that has been murdered by the dead spirit before the living man could be killed so in the end everyone's dead except the living man."

Scott kept asking questions like how long ago was the last time it was tried which was recorded and is any of the survivors still alive, but Simon only said that he had no idea and that Clary only told him very little about that trick.

Scott then left and so did Simon who just made up an excuse that it was late and he needed some sleep before training tomorrow.

I looked down at Clary's ruffled bed before walking over to it and picked up a photograph left on it.

I sat on the bed and studied the photo and smiled. It was the one of her and Luke laughing together in Central Park.

I turned the photo over to read the writing on the back of the photo.

I had to stifle my gasp as I saw a drawing of a weird rune or mark on the back of it.

Luke noticed and he asked me "Jace? What's wrong?"

I stared at the photo back before showing it to Luke and everyone else and I said "I don't know about you but I am pretty sure that the rune thing is freshly on the paper and I also believe that it means a lot more than nothing because Clary drew this and in a rush too."

Magnus looked at the rune and asked "So are you suggesting that it's a clue?"

I nodded and said "It must be, not even her brother would notice her quickly scribbling on a few pieces of paper or the back of photos and dropping them quickly to lead us to something. All you have to do is look carefully."

Magnus then stepped forward and frowned at the rune and asked to no one in particular "Does anyone actually know what the rune is by any chance? Because I've done all of my ancient rune courses and it's not one of those."

Everyone shook their heads sadly except one who stepped forwards and announced "I believe that I know where it's from."

Clary's point of view

Darkness, that's all I know at the moment, nothing else except darkness.

I murmured as I tried to climb out of the dark but it was like it just pulled me back into it's pits of darkness and leave me there.

I forced my eyes to open and it almost killed me as I was now looking straight into an extremely bright light.

I flinched away and exclaimed "Ouch." Or tried to but it came out more like "Oufshyf" as I had a binder taped over my mouth and I half groaned whilst saying it.

I had to blink a few times before my eyes adjusted to the now dimly lit room.

I heard a voice call "Sir, she's awake."

I tried to focus on the man talking but it was hard to see what he looked like except he had a massive pink scar running across his right hand.

Jonathan's voice then said through a walkie-talkie sort of thing "Okay bring her forwards for interrogation."

The mysterious man then grabbed my hips and hauled me up and I tried to scream at him "Watch your hands!" but again it came out slightly muffled.

The man had some kind of mask on his face so I couldn't see who it was but I made a motion to him trying to get him to take my mouth binder off.

He did as I asked and I coughed as I was practically pushed down the hallway.

The hand patted me on the back and he asked me "Can you die quietly please?"

I choked out "As you said please I will attempt to."

The man seemed to almost smile before turning cold again and he pushed me into a room with two chairs and a table in it.

He pushed me into a chair and he then chained and handcuffed me to the table and floor so I couldn't escape from this small dingy sort of room.

I looked at my guard person and asked him "Why am I here?"

He simply said "To be interrogated."

I muttered more to myself "Fun."

The door then opened and about six guards walked in surrounding my brother so that if someone shot at him it would be difficult to aim directly at him.

Jonathan sat opposite me and he said to me "Well Clarissa nice to see that you're recovering nicely. Nasty blow you had to the head."

I automatically answered sarcastically "Yeah the wall was very violent for a non-living object wasn't it?"

Jonathan glared at me and he said "You must want to know why you're here Clarissa is that correct?"

I answered "I know I'm being interrogated but I am indeed curious about what I'm being interrogated about."

Jonathan leant forward and he whispered "The missing pieces of the machine."

I felt strangely calm considering I had to quite literally kill or seriously injure people to get all of them pieces and I was also facing my demonic brother but I can hide my expressions pretty well so I knew that I wasn't showing any expressions.

I casually asked him "What about them?"

Jonathan now told me "We want to know where they are in the headquarters, and what guards them too. We know that you and your glittery and dark friends all went out to find them together but we want to know what you do to them afterwards."

I answered truthfully "I may have retrieved them but I now not where they are now. The Director used to take them and put them somewhere and I also don't know who guards the pieces either."

Jonathan nodded and said "That's it for today; put her back in her cell and I'll come and visit her later. And make sure she never finds a way out of that cell otherwise you're dead okay?"

My guard nodded and spoke to me "Right this way Miss."

He untied me before walking me back to my cell.

Once I was outside the cell he stood there staring at the doorway and I was extremely bored so I asked the man "What is your name?"

Then man almost glared at me as he answered with "My name is none of your concern. Got it?"

"Really? Nice name. Can I call you None for short?"

He apparently didn't get my humour as he just shoved me into the cell and shut the door behind him.

I went over to my bed and laid down on the cold metal surface and I thought about getting some sleep.

After about an hour my guard went away and no one replaced him so I was left alone.

Or so I thought.

A male voice said from the darkness "Who are you?"

I sat up and tried to locate the voice source but I couldn't find it.

I introduced myself "I'm Clarissa Morgenstern, Jonathan Morgenstern's sister but I prefer to be called Clary Fray. What about you?"

A figure stepped forwards and I saw a boy about Jace's age and he had very dark black hair and a really dark brown coloured eyes, he introduced himself "I'm Sam Penhallow, my mother follows the Morgenstern's but I didn't want to so they chained me up and shoved me into this place."

I asked more to myself really "Penhallow? As in Aline Penhallow's relative?

Sam nodded and said "Yeah, we're cousins. Why are you here then if your Jonathan's sister?"

I smiled bitterly and told him "I ran away from here when I was fourteen, I joined the CIA and I've been there for nearly three years now and I was on missions to get some of the pieces of the machine and well Jon got me from my bedroom by knocking me unconscious and that's the last thing I remember."

Sam nodded and he asked me warily "Do you have any food or water in your cell because I haven't got anything for two weeks now and I'm starving?"

I frowned and I walked to my food basket and I grabbed two bread rolls out of it before taking them to the bars between us and sliding a slim arm through the metal bars and handing Sam a piece of bread.

Sam's eyes lit up instantly and he stared at the bread for a few seconds before murmuring a quick thanks to me and then I had barely eaten three bites out of my own by the time he had gobbled it down.

I stared at him and saw just how hungry he must be so I handed him my piece of bread and said "Here you have it, you look like you could eat a horse."

As he took it and gobbled that down I went and gathered two cups of water for the two of us and I gave him a cup to.

After we finished drinking I put the cups back before sitting opposite Sam and asking him "Do you get questioned a lot?"

He shook his head and told me "No, I only have myself and my little sister Jasmine to talk to and now I have you too."

I smiled and we sat in silence until I heard a door open from the entrance to our line of cells.

I told Sam sharply "Get back into the shadows, now!"

Sam asked me uncertainly "What is it?"

I hissed at him quietly "Someone's coming towards us."

And now without another word he slid back into the darkness and I went and laid on my metal bed trying to fake sleep.

All I could do was hope that they would believe my lie and my friends and what you would call family at the headquarters found my secret so they know how to find me.

Sam's point of view

As soon as I first saw the red haired girl I knew that she was Jocelyn Fairchild's daughter. They shared the same red hair and small petite bodies and pale skin. The only difference that I could tell that they had apart was that this girl had a long thin pale pink/white scar running across her right cheek.

She looked unconscious which was normal and I was ready to talk to her as soon as she woke up again but when she eventually did she was soon dragged away for interrogation.

The girl came back about ten minutes later and she asked her guard "What is your name?"

The guard glared at her evilly "My name is none of your concern. Got it?"

"Really? Nice name. Can I call you None for short?" she half joked and I smiled slightly as she said that.

She didn't show how nervous or scared she probably was but the guard wasn't in the mood to joke around apparently as she just got shoved into her cell and then locked in again.

I stood in the shadows of mine and Jasmine's cell until the guard had disappeared probably to get drunk.

The girl was now lying down on her cold metal bed as though it was a soft feather made bed instead and she looked like she was almost asleep.

I decided that now would be a good time to talk to her so I asked her from where I was standing "Who are you?"

The girl shot up into a sitting position and looked around to find me and she kept looking at my spot but she wasn't sure but she still introduced herself to the dark "I'm Clarissa Morgenstern, Jonathan Morgenstern's sister but I prefer to be called Clary Fray. What about you?"

I stepped forwards and I could tell that she was staring at me and that I reminded her of someone in her past as I answered her question "I'm Sam Penhallow, my mother follows the Morgenstern's but I didn't want to so they chained me up and shoved me into this place."

She said softly as if she was asking herself that more than me "Penhallow? As in Aline Penhallow's relative?

I nodded and confirmed "Yeah, we're cousins. Why are you here then if your Jonathan's sister?"

Clary smiled bitterly and told me "I ran away from here when I was fourteen, I joined the CIA and I've been there for nearly three years now and I was on missions to get some of the pieces of the machine and well Jon got me from my bedroom by knocking me unconscious and that's the last thing I remember."

I felt slightly sorry for the girl, I know that Jocelyn faked her death and that Valentine hurt both of his children and Jonathan was abusive to her so it can't have been an easy life.

I nodded and asked her as I heard my stomach growl with hunger and my throat felt dry to "Do you have any food or water in your cell because I haven't got anything for two weeks now and I'm starving?"

Clary now frowned and she walked to presumably where her food basket was kept and soon enough she was sliding a slim arm through the metal bars and handing me a piece of bread.

I stared at the bread for a few seconds disbelievingly before saying "Thanks." And I gobbled it down which felt nice to have something to start to tame my hunger.

I looked back at Clary who had taken next to nothing from her bread roll and she was staring at me and then she handed me her piece of bread whilst saying "Here you have it, you look like you could eat a horse."

Clary then went and grabbed some cups of water as I ate and soon we were both drink our water too.

After we finished drinking Clart put the cups back before sitting opposite me again and asking "Do you get questioned a lot?"

I shook his head and told the small red haired girl "No, I only have myself and my little sister Jasmine to talk to and now I have you too."

She smiled and we sat in silence for a while.

Clary seemed to hear something as she sat up straighter and she ordered me "Get back into the shadows, now!"

I asked Clary carefully so she wouldn't harm anyone or herself "What is it?"

She hissed at me "Someone's coming towards us."

I froze as I realised that it must be either Jonathan or another guard so I melted back into the shadows as Clary made a fake sleeping position on her metal bed.

Now all we could do is wait for the person to leave before we could talk again and I hope that they will leave soon because there's something about Clary that calms me down so maybe just maybe she will be able to help me and hopefully I will help her out of here in return.

Jace's point of view

I watched as Luke studied the sign and then he turned to her bookshelf and pulled out loads of books whilst saying "She must have left this for me because she knew how much we would try to look for her and if I'm not mistaken it is from these books."

I glanced at the book titles which read stuff like 'Forests of silence' and 'Lake of tears' Luke flicked through the books until he found what he was looking for.

He showed me the book page and I saw the same sign written in the book.

In the corner of that page was a picture of a small dragon which Luke once again pulled out more books to prove it was them books and on and on we all went finding different signs which were connected to different books which then lead to another. As soon as the last book left the bookcase, the bookcase began to tremble and then there was a creak and the bookcase opened up on one side and we all just stared in astonishment at what we found.

AN: Sorry guys, I'm going to be really mean again and leave you there for now. Sorry again about how late I was to publish this chapter and I know that some people have been begging me to write more so this is mostly for all of you people who have enjoyed it from the start to now and I hope you guys all liked the chapter and also I was thinking about doing some small one shot stories on this story Clary's past like how she met Simon and how she and Simon ran away in a bit more detail than I have in this story. Please tell me what you honestly think of this story and also remember that I want your guys opinion on the other one shot/small stories of Clary's past too and if you guys are really lucky I might just do a few for some other characters. That's it for now guys please review and until next time I'm out.