Secrets by atlantisfan
Summary: He walks like his father, talks like his father but does he know it?
Categories: Fanfiction Characters: None
Genres: Angst, Baby!fic, Drama, Future Fic, Hurt/Comfort, Romance
Warnings: Character Death
Challenges: None
Series: None
Chapters: 7 Completed: Yes Word count: 7724 Read: 74810 Published: June 20, 2006 Updated: June 21, 2006

1. When He Found Out by atlantisfan

2. The Day Of Reckoning by atlantisfan

3. 1st Birthday Party by atlantisfan

4. Chapter 4 by atlantisfan

5. Joss' Father by atlantisfan

6. It was his fault by atlantisfan

7. Picking Up The Pieces by atlantisfan

When He Found Out by atlantisfan
Author's Notes:
I don't yet know how many chapter's this'll be, though the first few will all be set in the past and SHOULD be free of *evil cliffies*, i'll save those for later on. Thanks to teyla_emmagan for her beta. Also posted to my livejournal.
Title: Secrets
Rating: PG
Genres: Angst,Drama,Future Fic,Hurt/Comfort,Romance
Summary: The first time that he wanted to tell their secret was when he found out.......................
Word count: 566
Chapter Title: When He Found Out
Author's Notes: I don't yet know how many chapter's this'll be, though the first few will all be set in the past and SHOULD be free of *evil cliffies*, i'll save those for later on. Thanks to teyla_emmagan for her beta. Also posted to my livejournal.

********************************************************
7 years before

SGA-1 had just stepped through the gate from the genii homeworld, for once they had returned mostly unharmed and were all tired from the long negotiations.

‘Colonel Sheppard when you have a moment I would like to speak with you,’ was all she said before walking out of the gateroom.

He knew her well enough to know this was an indicator that something was up; normally she would be more than happy to see them and would want to know every detail of the day’s events – today was different. The rest of the team picked up on it as well; he could see from the slightly confused looks on their faces, handing his p-90 and vest to Teyla, he followed Elizabeth down the corridor.

From past experience he knew her favourite place was the balcony outside the gateroom, but as she had not headed in that direction he took his best bet and went down to the west pier.

Stepping out through the doors he looked straight ahead, there she stood arms wrapped around her body, trying to keep herself from being frozen cold by the chilling breeze. He approached her from behind and wrapped his arms around hers, pulling her backward and cradling her against his chest.

‘You okay?’ he asked, his thumb caressing her hand, ‘you just seemed a little off before.’
She stayed silent the only noise around them the wind as it rushed through their hair and past them.

‘Elizabeth?’ he questioned, turning her around in his arms to face him. Lifting up her chin he looked into her eyes and she looked back.

‘Define okay?’ was all she said before breaking eye contact.

‘Elizabeth?’ this time he held her firm so she couldn’t look away, he could see the tears starting to gleam in her eyes. As much as she tried she couldn’t lie to him, his face and body told her he was concerned, his eyes told her he was terrified something had happened to her.

‘We have a problem.’

‘Wraith?’ he asked genuinely, but from the way she looked at him he could tell it wasn’t, ‘bigger or smaller problem?’

‘Depends from whose perspective we’re talking,’ she said. Now he could tell she was upset, sarcasm was something he did and she usually looked down on.

‘I’m pregnant!’ was all she could say, pulling herself away from his grip she walked away.

John’s mind was racing; torn somewhere in between the excitement of the prospect of becoming a father and the consequences this could bring, not just to their relationship, but to their entire lives. The joy and adrenaline pumped through his heart at her words, but he could not think clearly. Grabbing her arm as she walked on he spun her gently to him.

‘Are you sure?’ Elizabeth answered John’s question with a nod.

‘How far along are you?’

‘Does it really matter John?’ she asked. He went to speak but she raised her hand to finish, ‘I’m your boss, you’re my subordinate - essentially we will both loose our jobs, Atlantis everything’ she threw her hands up in the air, gesturing to the magnificent city around them.

He pulled her into a tight embrace and kissed her on the forehead, ‘everything will be okay, don’t worry, Lizabeth.

‘How?’ she murmured into his shoulder.

********************************************************
The Day Of Reckoning by atlantisfan
Author's Notes:
Thanks again to teyla_emmagan for beta-ing. Please read enjoy and review.
Title: Secrets
Rating: PG
Categories: Fanfiction
Genres: Angst, Drama, Future Fic, Hurt/Comfort, Romance
Summary: Then, the hardest part.....................................

********************************************************
6 years 4 months before

Elizabeth and John were asleep in her room. At 8 ¾ months pregnant she knew the baby could come anytime, so it had been made a permanent fixture, one of her friends would stay in her room every night.

‘‘Lizabeth are you okay?’ John turned to her, wrapping his arms tighter around her wriggling body. Unlike the rest of her ‘friends’ John tended to leave the camp bed on the floor untouched and sleep next to her.

‘I don’t know,’ she exhaled loudly, ‘ I can’t say I’ve had any experience, but I would say this baby is going to come tonight!’

John’s eyes immediately widened, ‘Really!!!! We should probably get you to the infirmary then.’ Untwining their arms and legs John sat up, climbed out of the bed and began to pull on his clothes.

‘I’m fine John,’ she moaned rolling deeper into the bed, ‘anyway Carson said not to come to the infirmary until my water has broken.’

‘Yeah, but I want to be on the safe side, it’s me who he’ll blame if you’re not there exactly when you need to be.’

‘John calm down anyway…..UH OH!!!’ Elizabeth sat bolt upright.

‘What???’ John rushed straight to her side and held her hand as she turned and climbed to sit on the edge of the bed.

‘Okay, maybe your right….water’s broken!!!!!!!!’

‘Stay there,’ John said pointing at her. He searched under his jacket on the floor until he found his earpiece; placing it on his ear he called Carson, ‘Carson this is Sheppard, Elizabeth’s water just broke.’

Turning around he found himself staring at Elizabeth who was putting on a t-shirt and jeans, he couldn’t believe this was really happening; he was so excited and nervous that he was becoming a father.

But then he remembered their arrangement, biologically he was becoming a father, but their rule was that Elizabeth would bring up the child and John could help as a friend, basically the child would not know him as it’s father. This hurt him a lot but it was the only way that he and Elizabeth could stay together on Atlantis with their jobs and reputations intact. As much as he hated it, it was the only way.

Ironically the birth was something that they both looked forward to, but hated the thought of, manly because they needed to keep their heads and not get carried away, just to make sure that their relationship would not become the subject of a court martial.

********************************************************
Later in the Infirmary

Elizabeth was in labour and had been so for the past 8 hours, she had been given an epidural but this was still a very terrifying and painful experience for her. John sat at the side of her bed, their fingers intertwined and they grasped onto each other for support, her little more than him.

‘Elizabeth lass you are gonna need to push now, can you do that for me?’ Carson asked calmly and contently.

‘Uh, I’m not sure……I…..uh can,’ she panted, squeezing John’s hand harder.

Carson’s face looked worried, ‘come on Liz lass, you can do this,’ looking to John ‘and John’s here to help you.’

John stood up and pulled Elizabeth’s head to his chest cradling it, ‘sssshh,’ was all he said as he kissed her on the head and traced out pattern’s on her hand, ‘I’m here for you no matter what!......... stick your nails into my hand or whatever as long as it helps you and the baby – that’s all that matters.’

Noticing how Carson had turned his head away at this point John decided to step back from holding Elizabeth and sat back down. He felt sort of put down and oppressed by the fact that the doctor had seen how much he cared for Elizabeth and that he had felt he had to step away. He realised at that point just how hard it was going to be one the baby came.

Carson turned to Elizabeth, ‘okay, when the next contraction hits I need you to push as hard as you can to get this wee one out.’

She responded with a nod and when the next contraction hit John felt her nails sink into the skin on his hand as she pushed with everything she had left. The atmosphere of pain and anguish was broken with the small cry of a baby that Carson was cradling; holding up the scissors he offered them to John. John looked to Elizabeth to get her permission, which he got in an instant, and taking the scissors he cut the umbilical cord.

‘So lass, you got a little boy and he’s perfectly healthy,’ he said handing the baby in a blue blanket to Elizabeth, ‘he’s got your dark brown hair and defiantly John’s eyes and nose.’ He tapped his nose knowingly.

‘Thank you Carson, thank you so much’ replied Elizabeth as she looked down on her son with a caring expression on her face.

‘That’s okay lass, it’s my job,’ Carson caught a glance at John, ‘I will bring you the birth certificate to fill in and sign,’ and left the room.

John looked on as Elizabeth sat there cradling his son, their son in her arms and stroking his face gently, inside he felt a rush of love for this child but also a jealousy of Elizabeth because she would get to bring him up, while he didn’t. Elizabeth knew John well enough to know exactly what he was thinking.

‘John, if you don’t think you can do this please tell me now, I don’t want to be responsible for causing you all this pain……… John?’

‘‘Lizabeth I’m fine, you know I will be….’ he trailed off, ‘it’s just it might take some time to get used to him being my son without me being there for him.’

Elizabeth swallowed seeing what this was going to do to the man she cared for so much, ‘do you want to hold him?’

John stuttered for a moment, ‘yes, I would love to,’ as Elizabeth slipped the baby into his arms Carson came back into the room.

‘I forgot to ask, what are you going to call him?’

Elizabeth and John looked to one another; Elizabeth had wanted to call the child Sasha or Alexander, whereas John had preferred Matthew or Joshua for a boy.

‘His name is Joshua Alexander John Weir,’ she announced, ‘Joss for short.’

‘‘Lizabeth, you don’t have to, it might arouse suspicion.’

‘If I want to name my son after the person who was there for me when I gave birth then I will John, I don’t care what people think, and I want you to have some paternal link with him.’

‘I don’t know what to say…. or how to feel’ he said looking down at his son Joshua in his arms.

‘Then don’t,’ beckoning him he came to her side, perched on the bed.

Wrapping her arms around his neck she pulled him into a kiss over the face of their newborn so,. John had never felt more emotion towards two people than he did then, there was nothing he wanted more than to marry Elizabeth on the spot and announce the birth of their son to the world. But, he couldn’t, and that was what was the most painful moment and the worst feeling of his life!!

********************************************************
1st Birthday Party by atlantisfan
Author's Notes:
I'm hoping that we should have two more chapters set beforehand before we move onto now- which i'm guessing will be 3/4 chapters long. Anyway read and review.
********************************************************
5 years 4 months before

Being the boss’ son Joss was probably by far the most known, loved and popular child in Atlantis at the time, so when it came to his 1st birthday, although he would never remember it, the Atlantis personnel couldn’t resist but give him a massive party in the gateroom – probably just another reason for a big party. There also seemed to be a massive excess of presents scattered across the gateroom floor along with banners and balloons scaling the walls. Elizabeth would probably have not have been surprised to find out that John was behind the whole thing.

Elizabeth was sitting on the gateroom steps with Joss sitting on her lap when John walked in to the room, seeing her he went over and greeted her.

‘Elizabeth,’ he smiled at her and waved to Joss.

‘So can I assume that you are solely behind the planning of this or did you have partners in crime,’ she teased.

‘‘Lizabeth, I hardly think crime is the best word to describe this situation.’

‘John, how are you?’ she asked looking worried.

‘Really I’m fine, better than fine, after all I get to plan the biggest birthday party ever for my so….. favourite member of the Atlantis personnel.’ He cringed at his slip of the tongue. She nodded her head towards her office and handing Joss to John they walked upstairs to find somewhere more private to talk.

‘I’m not stupid John, I know we haven’t had much time together recently but I can see that this is getting to you.’

‘Yeah it is, but I am letting this get to me and we’re in too deep to do anything to change the situation. I’ve got to learn to live with this!’

Downstairs Rodney had picked up the microphone and started talking, as he usually did and began calling out for Joss and Elizabeth to come up to the front. Elizabeth didn’t want to leave John in the middle of their discussion as he was opening up to her but she really didn’t have much option.

‘Look, I promise you can spend some time with me and Joss tonight,’ she sealed the promise with a quick kiss and taking Joss from him.

It was at the point when she took Joss from him that it hurt again, this was his son’s 1st birthday and it was something he’d rather celebrate as the proud father. Calming himself down, he composed himself before walking out of her office and joining the party that was just beginning downstairs.

It was then that Elizabeth was asked to give a little speech on behalf of Joss. ‘So, what to say well, I guess the past year has been the best year of my life, becoming a mother is probably the best thing that has ever happened to me and I’ve enjoyed every second of it,’ smiles appeared around the room. I guess my one bit of advice to you all is don’t become single parents intentionally and try to run a city at the same time,’ laughter filled the room, ‘but luckily I have my closest friends, John, Carson and Rodney to thank for helping my out, I wouldn’t have been able to cope without you guys.’ Rodney stood up on the stairs to get recognition from the audience. ‘Yes everyone, I let Rodney hold my baby.’

There was again another outburst from the room; Elizabeth continued to speak as John quietly snuck out of the back. This was overwhelming for him, this was his son’s 1st birthday and he would have to celebrate it as a bystander. He didn’t notice that she had finished speaking until a concerned voice appeared from behind him.

‘John, are you okay?’

He stood there in the corridor thinking very carefully over those three measly words.

‘Are you okay?’

That was all she ever seemed to ask him these days, she was so wrapped up in everything she had, and she couldn’t understand how he felt. There were times when he knew she tried but couldn’t give him everything that he needed. After all this was his idea, concealing that he was Joss’ biological father was the simplest way around their problem, for her anyway.

A little voice inside his head was screaming out to tell everyone the truth about their relationship so that he could get to know his son, but at the same time his brain was telling him that it was insane for him to even consider it, the consequences would be dire for the both of them. He wanted to turn to her but he couldn’t, sensing he was about to cry he started to walk off down the corridor.

‘No,’ he called out as he walked off.

********************************************************

A/N - ooooh, that was short and a little more angsty, going to try for a longer chapter next. Almost forgot thanks teyla_emmagan for beta-ing
Chapter 4 by atlantisfan
Author's Notes:
Okay wasn't that much longer, i moved the rating upto PG-13, i haven't actually written anything to warrant doing so but just implied. Thanks again to teyla_emmagan for beta-ing.
Title: Secrets
Rating: PG-13
Categories: Fanfiction
Genres: Angst, Baby!fic, Drama, Future Fic, Hurt/Comfort, Romance
Summary: When Joss starts to become more like his father, he can't help but notice.................
Word count: 1031
Author's Notes: Okay wasn't that much longer, i moved the rating upto PG-13, i haven't actually written anything to warrant doing so but just implied. Thanks again to teyla_emmagan for beta-ing.

********************************************************
4 years before

Elizabeth had asked John to look after Joss for a few days whilst she was away on negotiations on a nearby world. Surprisingly John and his team had not been asked to accompany her, but this as he speculated was probably because she didn’t want to leave Joss with anyone but John for such a long period of time and as usual saw the danger to herself as rather minimal.

By now Joss was 2 years 4 months old, was very active for his age and had been irritating John all day, the usual for a little boy. But was now finally fast asleep in Elizabeth’s quarters, John was lounging on her bed and was slowly drifting off to sleep as well.

He went into the other room to sit by his son as he slept, and watched the rise and fall of his tiny chest as he breathed; feeling John’s eyes on him Joss woke.

‘John, what you doing?’

‘Nothing Joss, just go back to sleep okay, I promised your mum that I’d make sure you were asleep before I went to bed,’ he smiled and stroked his son’s sleepy head.

‘When is mummy come back?’

‘‘This child is relentless he thought, carries some characteristic familiar to yourself.’ He had learned to live as Joss’ friend and one of his many ‘uncles’ on Atlantis, but every now and then, he recognised himself in his son or something was said that brought back painful memories, and it hurt.

‘She’ll be here in the morning when you wake up,’ John said patting down the ‘bed hair look’ that Joss had also inherited, ‘go to sleep now, and whatever you do don’t tell your mum I took you off Atlantis, okay.’

Joss nodded, ‘thanks John,’ and slid off into a peaceful sleep.

John found himself asleep on Elizabeth’s bed only moments after his son.

He was woken by the familiar musk scent of Elizabeth’s perfume as she entered the room, placing down her bags she went into Joss’ room to check on him. John got out of bed and followed her; standing behind her at the doorway he slowly enveloped his arms around her.

‘Hello gorgeous,’ he pulled her back to lean against him.

‘Not so bad looking yourself,’ she used her usual flirtatious manner with him.

‘He looks so beautiful and peaceful when he sleeps,’ John commented.

Elizabeth was thrown for a moment, forgetting that watching Joss sleep was not a luxury John had every night, ‘yeah, he is,’ she agreed.

‘Thank you for letting me look after him, it’s been a hectic but eventful and enjoyable few days.’

‘I wouldn’t want anybody else to John,’ she turned and looked up to him, ‘he’s your son and some day I want him to know that, but for now I want you to spend as much time getting to know him and vice versa.’

Breaking the silence in the room John let go of her and said, ‘I think I should get going now,’ he went back into her room to get his stuff.

Elizabeth was shocked by this and in a way so was he; she had expected him to stay the night and he had expected her to ask him. Following him out into the small corridor she stood near the door. As he passed her she grabbed his wrist.

‘Please John, don’t leave.’

It was all she said, but it was all he needed. It made him feel for once like he was safe and at home with her. Reaching forward he caught her chin in his hands and lowered his face down next to hers and leaned in.

They stumbled kissing backwards into her bedroom, almost knocking over his bag in the hallway and, tripping over her bags at the doorway to her room; they landed unceremoniously intertwined on her bed. Both laughed and melted into one another, tongues and bodies dancing into the night.

********************************************************
The next morning

John woke up with the light coming through the windows to find Elizabeth asleep curled up onto his side, he pressed a kiss to her forehead before detaching himself from her and climbing out of bed in search of some clothes. Once dressed he went back over to her to find her awakening, leaning forward he kissed her long and passionately only pulling away when they were interrupted by a small child entering the room.

‘Joss?!?’ Elizabeth murmured into his mouth.

John pulled immediately away when he saw him, he felt ashamed that his son had seen them together, it would confuse him.

‘Hey there mate,’ he smiled reassuringly but Joss remained silent.

‘Morning darling,’ even Elizabeth seemed a little lost for words at the awkwardness of the situation.

‘Are you my daddy?’ his voice was quiet but not as quiet and long as the silence that came afterward.

‘I…uh...I,’ he looked to Elizabeth for support.

His heart crumbled and he felt his body buckle beneath him, now he had to outright lie to his son. He didn’t know what to do, so much he urged for Joss to recognise who he really was but at the cost of all of their way of life. He was in agony, but this was not like he was used to, this type was way more painful.

‘No!’ Elizabeth said firmly, ‘he’s not, but you must not tell anybody what you saw here or that John was here this morning! Okay baby?’

Joss’ face fell at her words, it was obvious that even at almost 2 ½ Joss had grown greatly attached to John and wished that he was his father. John couldn’t look either Elizabeth or Joss in the face; the anguish he felt was far too much, picking up the rest of his clothing and his bag from the hall he almost ran out of her door. He had almost convinced himself by now that Joss did not have a father.

********************************************************

A/N - I'm thinking this is the last of the chapters set in the past - it can only get more angsty.
Joss' Father by atlantisfan
Author's Notes:
Thanks to my beta teyla_emmagan
Now we're getting into the real story........................
Title: Secrets
Rating: PG-13
Categories: Fanfiction
Genres: Angst, Baby!fic, Drama, Future Fic, Hurt/Comfort, Romance
Warnings: Character Death
Summary: He walks like his father, talks like his father but does he know it....................................

********************************************************

Now…………

Four years on at nearly 6 ½ Joss was running through the halls of Atlantis trying to find his mum, he had just finished school with the few other Athosian children that are living in the city and was looking forward to seeing John, who was due to come back from a mission in around two hour’s time.

He valued John as on of his best friends; most of the Athosian children were at least 4/5 years older than him or were really young and most spent as little time with him as possible as they liked to be with the other Athosian. Also he looked up to John, he had never known or had a father figure so John was as close as he could get, he was also not stupid and knew that John and his mother were closer than they liked people to think.

John was also the only person who had taken him out in a jumper or through the stargate, though admittedly he did do this behind his mother’s back.

Rushing around the corner he bumped into Dr. McKay, he didn’t really like the man, Joss knew he is very intelligent and a good friend of his mother, he also knew that Rodney was a very busy man and had little time for kids although he was considerably nicer to him than the other Athosian children. Plus the fact John has told him that Rodney was annoying and very smarmy – not that he knows what that word means.

‘Oh, shit,’ he swore loudly as his coffee flung out of his hands and landed on the floor, ‘look where you’re going kid, you could’ve spilt the coffee all over my work,’ indicating to the large folder in his hand.

‘Sorry Rodney.’

Joss began to walk off, Rodney also had a large ego and rather a liking for over-exaggeration – ‘I really should get mum to tell me what this means’, he thought as he walked away. He also knew never to take Rodney seriously.

‘Oh, so you’re not going to help me clean this up,……Hey!……Hey!’ ‘You wait until I tell you’re mother that you attacked me in the corridor and didn’t help to clean up.’ the scientist yelled after him.

Joss simply walked away and holding his hand up in the air he waved to Rodney, like John, he had no respect for rules or authority - especially certain scientists. Following the corridor along he came to the gateroom, his mum had told him never to go in there without an adult, but he was bored and well, she was in there!

********************************************************

Walking up to the door it swung open for him, another thing he had in common with John was a strong ancient gene, which John of course had taken the liberty of teaching him to use.

‘Wow!’ he exclaimed as he entered the room, normally he was ushered through here and never got to spend time looking around.

Climbing up the steps, opposite the gate, he went into the control room where he saw Dr. Zelenka and a few other Atlantis members that he vaguely knew.

‘Dr. Zelenka?’ he asked, the man raised his head from his work to look at Joss.

‘Should you be in here Joss?’ he replied.

Joss raised his hands up in the air and pulled a face of confusion, pretending to be naïve. ‘Dunno?’ Lowering his hands he continued, ‘so can you tell me when John will be back? It’s just I really want to spend some time with him.’

‘He’s due back in about an hour, but your mum will want to debrief first and then the team will have a check down in the infirmary and want to get cleaned up, that’s if he doesn’t come back injured of course!’ ‘Tell you what Joss why don’t I send him to find you when he’s finishes up here?’

Joss looked down to the floor and feigned being upset, ‘I just wanted to wait here for John that’s all.’

‘If you promise to stay out of the way then you can stay.’

Joss smiled but his moment of getting exactly what he wanted was broken when his mother stepped out of her meeting with Colonel Caldwell on the other side of the room ended.

‘Joshua Weir, what the hell are you doing here?’

‘Shit,’ swore Zelenka, that kid had him hooked every time.

Grabbing Joss’ hand Elizabeth apologised to Caldwell and the rest of the gateroom before leading him down the stairs, through the doors and out into the corridor.

********************************************************

In the corridor she pulled him to a halt.

‘Joss,’ she reprimanded, ‘how many times have I told you that the gateroom is a dangerous place and that you are only to be there under adult supervision?’

‘Dr. Zelenka was there!!! And so were you!’

‘Joss, don’t play me, why were you in there?’

‘Okay, I was waiting for John to come back ‘cause I’m bored.’

‘Tell you what Joss, if you’re that bored why don’t you go and play with the Athosian children?’ Seeing the look that appeared on Joss’ face she could see this wasn’t something he was enthralled by the thought of, ‘Do you want me to do something with you?’

Joss shook his head, and Elizabeth was hurt, for the first time in her life her son had openly rejected her in favour of John. Maybe now she thought this was payback for what she had done to John, well not necessarily what she had done, but what John felt.

‘Mum, when is John going to come back?’

‘Your fathe…..’ Elizabeth corrected her mistake as quickly as possible but not before Joss had noticed, ‘John will be back in around an hour.’

‘WHAT?!?’ Joss turned and looked his mother in the eye, ‘I thought you told me many times that John was not my dad!’

Elizabeth began to panic, ‘Joss, he’s not, he is not your….’

She was cut short by an announcement on the system,
Unscheduled Activation followed by the sound of her the stargate coming to life and
‘We’re coming in hot’ it was John’s voice over the radio.

Hearing this Joss broke into a run back towards the gateroom, the doors parted and there coming through the gate at that second came his father, firing off rounds whilst the last members of his team came through.

Out of the corner of his eye John saw Joss come running into the room, all he heard were the words ‘Dad’ repeated over by his son who despite the weapons fire continued to run towards him.

‘GET DOWN!!!!!!!’ he screamed, running towards Joss to cover him. A shot that contacted his shoulder caused him to buckle down, but he kept moving across the room.

Everything seemed in slow motion for a moment, as he buckled to the floor John heard the sound of two bullets narrowly passing his ear, looking onward he saw Elizabeth arrive at the door just in time to see Joss be struck twice in the chest and fall to the floor.

********************************************************

A/N - IS THAT THE END?
left you on an evil cliffie there.....oh so evil read and review if you want me to help Joss out!
It was his fault by atlantisfan
Author's Notes:
sorry about the evil cliffie before!!! i just couldn't resist!!!
thanks to teyla_emmagan for beta-ing
Title: Secrets
Rating: PG-13
Categories: Fanfiction
Genres: Angst, Baby!fic, Drama, Future Fic, Hurt/Comfort, Romance
Warnings: Character Death
Summary: He walks like his father, talks like his father but does he know it?

********************************************************

Previously:
Everything seemed in slow motion for a moment, as he buckled to the floor John heard the sound of two bullets narrowly passing his ear, looking onward he saw Elizabeth arrive at the door just in time to see Joss be struck twice in the chest and fall to the floor.

And Now...................

Elizabeth’s scream filled the room as the gate was shut down, both she and John ran to their son’s side. The entire control room looked on in bewilderment at what had happened, to John everything seemed to spin and disappear around him apart from his son lying there out cold on the floor and Elizabeth’s screaming. Somewhere he could hear other people gasping, the voices of his team and the control room swearing, and many people calling on the radio for medical help.

The tears streamed down his face as he grabbed Joss’ hand, somewhere above him he heard Carson arrive cursing and some marines pulled him and Elizabeth away from their son. Elizabeth reached out and clung to John. Pulling each other up and holding onto each other for dear life they made their way down to the infirmary.

********************************************************

In the infirmary Elizabeth had to be sedated when she wouldn’t let John have his shoulder looked at and because as much as she needed to, she wouldn’t calm down.

Joss was in surgery for 4 hours, one of the bullets had gone right through his lung and was locked in the back of it, and the other was in his heart.

Carson walked out of theatre 4 hours later in search of Elizabeth and John; this was very hard for him as he had brought Joss into the world 6 ½ years before hand and covered for them by keeping Joss’ birth father a secret, but it would seem that secret did no longer need keeping. He found Elizabeth sedated but awake in the infirmary, John was sitting on the other side of the bed.

‘Elizabeth, John………I am so sorry, but we lost him in theatre about 20 minutes ago.’
Carson was lost for words as the tears streamed down his face, but Elizabeth and John remained silent, in shock.

Elizabeth’s body began to shake in terror and grief, fighting desperately against the sedatives to move. John felt tears once again stream down his face; he gripped onto Elizabeth’s hand to try to comfort her, just like he had the night Joss was born. She started to cry and screamed out loud.

‘I want my baby, Joss!’ she continued to scream until Carson administered some more sedative, this time enough to knock her out for a few hours.

‘Take me to see Joss, Carson.’

‘It’s not a pretty site son, are you sure you want to?’ John nodded.

‘He’s my son Carson; I at least owe him that.’

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John sat beside Joss’ body, cradling his dead son’s head in his arms he sat there and wept. A million thoughts ran through his mind, the most important and most prominent was that it was all his fault! This was his fault! - If he had moved quicker he would’ve taken the bullet instead. - If they hadn’t lied, Joss would never have run into the gateroom, he would never have been shot. - They would probably be as far from Atlantis as possible, Joss would be as far from the danger as possible. - They could’ve been a normal family, the thought of that seemed a million miles from there at that moment. - Didn’t they do all this for Joss, didn’t they stay on Atlantis, and didn’t he suffer giving up Joss so that he could have an important exciting life. - If this was all for him, if it ended like this, was it all worth it?

John left Joss’ body, it was his fault, and as much as blaming himself wouldn’t help it made him feel better. Walking into the infirmary he was greeted with a sea of faces all bringing their apologies and grievances, most of them however aimed at Elizabeth who was still out cold, only a select few who were in the control room at the time knew that he was the father. Rodney came up to him.

‘Sheppard, I had no idea, I’m so sorry’

John walked straight passed him, all this it meant nothing to him, he had wasted nearly 7 years of his life on a his child, to have it all end like this – nothing could ever change the way in which he felt at this moment. He had all those chances before hand to share with his son, all those things to experience as a father, which could never happen. John headed straight to his room and systematically began to destroy everything he owned from posters to his beloved guitar, smashing it on the walls, cutting it with scissors and shooting posters and pictures on the walls. Somewhere in the midst of all this he collapsed from sheer exhaustion onto his floor.

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A/N - should be just one more chapter left. please review and tell me what you think.
Picking Up The Pieces by atlantisfan
Author's Notes:
this should be my final chapter so hope everyone liked!!!!!!!!!!!
Title: Secrets
Rating: PG-13
Categories: Fanfiction
Genres: Angst, Baby!fic, Drama, Future Fic, Hurt/Comfort, Romance
Warnings: Character Death
Summary: He walks like his father, talks like his father but does he know it?

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Previously......

John walked straight passed him, all this it meant nothing to him, he had wasted nearly 7 years of his life on a his child, to have it all end like this – nothing could ever change the way in which he felt at this moment. He had all those chances before hand to share with his son, all those things to experience as a father, which could never happen. John headed straight to his room and systematically began to destroy everything he owned from posters to his beloved guitar, smashing it on the walls, cutting it with scissors and shooting posters and pictures on the walls. Somewhere in the midst of all this he collapsed from sheer exhaustion onto his floor.

And Now............

John woke to the low murmur of the sea’s waves lashing against the city’s walls. His body ached all over from the crumpled position in which he had slept on the floor. Surrounding him was the mass of destruction that he had caused the night before – and then it all came flooding back to him.

The hundreds of faces of all the people he had ever hurt flashed before his eyes, despite all the other faces, those of Elizabeth and Joss remained glued to his mind. They were the ones he had hurt, let down the most. His little boy Joss, who he had failed in every way, who had been killed by part of his father’s everyday life; he was beginning to see how General O’Neill may have felt. But, this was not the same, this was not earth, he was in the lost city of Atlantis, not on earth. There must be something he could do with all the technology around – his son should’ve already been saved. Then it occurred to him, it was not the technology that could help him, if they had been able to use that they would’ve done it by now, but the people – the Ancients.

He stood up like a bolt of lightening had struck him, breaking into a run he sprinted through the corridors to the gateroom.

Up in the control room was one of John’s air force lieutenants.

‘Lieutenant,’ John shouted, the young man turned to face him.

‘Yes sir.’

‘Dial the gate for M6X472’ (the planet from epiphany)

The lieutenant seemed a little unsure, ‘does Dr. Weir know about this sir?’

John was becoming impatient and he saw the lieutenant radio for some help dealing with him, he seemed a little hesitant, ‘I’m sorry sir, but Dr. Weir doesn’t want anybody else out on missions at the moment.’

‘This is a direct order lieutenant, I am telling you to dial the gate!’

‘John?!’ Elizabeth was standing just inside the doorway to the gateroom, her face tired. He could hear an intake of breath from some of the staff; this it seemed was the first word she had said to anyone since hearing of her son’s loss.

‘I need to do this,’ he looked at her, ‘for me…..’ he trailed off.

‘I’ve already lost my son; I do not want to lose you as well. Please don’t do anything stupid?’ her eyes pleaded with him, but he would not, could not give in and he couldn’t explain either.

‘Dial the gate lieutenant,’ she said as she turned on her heel and walked out of the room.

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Determination in his stride, John stepped swiftly though the gate and didn’t look back as it shut down behind him. He made his way to the now empty village where he had spent 6 months living over 8 years before. Looking around he began to revoke old memories of his time here, whilst he was living with Teer and her brother Avrid. Standing in the centre of the village he began to call out her name.

‘Teer,’ John’s voice was continuous, ‘Teer!’

With no response, John sat down on the ground and continued to call her; he was not going to be moved until he had at least been acknowledged by her – she and her people at least owed him that, he had helped them to ascend. A woman’s voice broke his train of thought.

‘John,’ Teer said, she stood in front of him, not a tiny feature different from how he had known her before. He went to answer her, but she cut him short.

‘There is no need to tell me, I already know what happened and why you are here. I am very sorry, John, for the loss of your son, but there is nothing I can do.’

‘What?’ John was confused, ‘but, you’re an ancient, you ascended, you can do anything you want.’

John jumped to his feet and stared into her face, flinging his arms in the air around him. The expression on his face somewhere between grief and anger.

‘Theoretically,’ she paused, ‘I could bring him back.’ John’s face lit up, but fell at her next words.

‘But what would be the point? I have seen the life that you and Elizabeth gave him and I cannot be held responsible for bringing your child back into the life he had.’

John fell to his knees in front of her and looked up; his eyes begged her to help him with all the strength he had left. ‘Please Teer, I will do anything, I uh…. I will trade my life for his if I have to, if it is what it takes,’ he spoke with such conviction but Teer did not falter, though it seemed he had shocked even himself with his suggestion.

‘That’s almost exactly my point!’

John’s face was confused so she qualified herself.

‘Your son wants nothing more than a father in his life, his father; he wants you to be his father – he wants the one thing you claim you cannot offer him.’

The tears now flowed freely down John’s face as he realised what Teer was saying to him. ‘I….I want nothing more than to be his father, to be able to do father-son things with him,’ he choked out.

Completely unable to control his emotions John felt his body give way beneath his and he slumped to the floor. Teer reached out to him and lifted up his chin, kneeling down beside him she looked through the tears into his dark eyes.

‘Then go back to Atlantis and tell him!’

John looked at her in awe.

‘But, you have to be honest and open; in the long run it will hurt him even more to keep your secret to himself. The people of Atlantis will be there to support you, as will I.’
Teer pulled him up from the ground with her, ‘be honest with her as well!’

John nodded his head, so lost from words as Teer disappeared into a white light that seemed to envelope them both.

John opened his eyes again and found himself lying on the ground in the centre of the village. Memories of Teer’s words flooded back to him as he stood up and sprinted back to the gate.

His heart pounded in his chest as he stood in front of the gate, if Teer’s words were true then it meant he and Elizabeth would have another chance with Joss, a chance to be honest with him. However as the gate came to life his body was filled with nothing but fear, what happened if he went through and all of this had been in his head – everything would be as he had left it, Joss gone and his and Elizabeth’s lives most probably shattered.

As he stepped through the gate he prayed to anyone that was listening that Teer’s words were true. In a moment he stepped into the Atlantis gateroom, anticipation running wild through his veins.

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Looking up he could see a large amount of the Atlantis personnel crowded around the room, his mind stuck somewhere between the similarity of the day of Joss 1st birthday and the fatal previous day.

His eyes scanned the room for Elizabeth who was not in her normal position. They found her standing on the staircase, smiling brightly at him. She was smiling. John felt his heartbeat quicken; everyone was looking as if they were waiting for something to happen.

Out from behind Elizabeth stepped Joss – a very much ALIVE Joss!!!!!!

‘Dad! Dad!’ Joss shouted out to him.

John was overwhelmed with emotion; he felt his heart crushed into tiny pieces at Joss’ words. Bending down he picked Joss up and swung him around in the air in a tight hug. He had never felt as proud as he did at that moment, he and his son finally united in front of everyone, nothing had ever felt so right.

John stopped swinging his son and put him down as Elizabeth approached them. Placing Joss steady on his feet he found a pair of arms grab round his leg stopping him from moving. Elizabeth was giggling at the sight and reaching out to her, he pulled her against him and into his arms.

‘I love you,’ he whispered in her ear.

Without giving her a chance to answer him, he pulled her flat against his body and into a breathtaking kiss. When she didn’t resist the Atlantis personnel burst into applause around them, wolf whistling and cheering at them.

Pulling away she looked up at him and caressed his cheek.

‘I love you too!’

Prising Joss from his leg, John took the chance he had been waiting almost 7 years for, bending down onto one knee he spoke.

‘Elizabeth Weir, will you marry me?’

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A/N - fini hope all liked. please review, comments are love!!!!!!!
finally i would liek to thank teyla_emmagan for all her help with titles, chapters and for most importantly for beta-ing.