Disclaimer: I don't own Stargate Atlantis or SG1

4 Months later

Elizabeth sat in her office at the SGC. She placed a hand over her swollen abdomen and lightly rubbed it. The baby, as if sensing her, kicked where her hand was placed. Elizabeth smiled at the feeling. He was going to grow up like his father; she knew it.

She didn't know the sex of the baby but John always referred to the baby as 'he' and she wondered if he knew. John's visits had slowed in recent months. He usually tried to see her once a week, but slowly that had decreased to once every few weeks, until the point where she hadn't seen him in a month.

She had theories, one was the other Ancients had banned him from seeing her and the other was it was getting to painful for him to see her grow, knowing he'd never be able to know his child. Elizabeth wished that he would come see her but she knew it was difficult for him.

She looked back at the papers on her next. Treaties with different races of people, a new treaty with the Tok'ra. It was utterly boring. Elizabeth placed her head in her hands and sighed.

"Tired honey?"

Elizabeth looked up and smiled when she saw John smirking at her.

"Hey, I know you. You got me pregnant then disappeared."

John cringed

"Yeah, sorry, I've been meaning to come and see you. It's just…"

"…that it's difficult?" Elizabeth finished for him; John smirked at how well she knew him.

"You know me too well"

Elizabeth smiled at John for a moment before her smile fell; this was always difficult. He'd come and see her but have to leave too soon. There was never enough time for them. She looked back down at her papers; this was uncomfortable for both of them, John looked down for a moment before looking back at her.

"How is he?"

Elizabeth smiled

"He's fine."

John walked round to her and did something unexpected, he placed one of his hands on her abdomen and the baby kicked.

He hadn't touched her since the night he ascended and came to see her. She always figured he couldn't have contact with her.

"John…"

"Shhh, he can sense me, he knows I'm here."

Elizabeth was suddenly very grateful she didn't have a security camera in her office, explaining that she was having visits from her dead ascended fiancé and not telling anyone might put Jack in a bad mood.

Elizabeth lowered her hand and placed it on top of John's. John opened his eyes and looked at her. For the first time in his eyes, she saw hurt, pain and longing.

He placed his other hand on her cheek and Elizabeth closed her eyes, she felt him come closer to her; he lightly pressed his lips to hers. As she felt him pull back, she opened her eyes and saw that he was gone.

She placed her hand on her abdomen where his hand had just been.

The door to her office swung open and Daniel walked in

"Elizabeth, Jack said he needed the Tok'ra treaty…" He saw the tears in her eyes and walked over to. "…Elizabeth are you okay?"

Elizabeth nodded and turned to her desk.

"These are the papers"

She handed him a stack of papers and turned back to what she was working on before.

Daniel put the papers back down and leant against her desk facing her.

"Elizabeth…you know where here for you right?"

Elizabeth nodded keeping her eyes on the papers in front of her. She wanted to tell someone she was seeing John because she was slightly afraid she was going insane and that John wasn't coming to see her, that it was just her imagination. But she was afraid that if he really was coming to see her and she told someone the other Ancients would stop him from visiting. There was about three months to go until she gave birth and she knew that after that John wouldn't be able to visit anymore and she couldn't bare loosing the chance to see him any earlier.

Daniel placed a hand on her shoulder and she looked up at him. Daniel had genuine concern in his eyes.

"Elizabeth, I know how difficult this must be for you. I lost my wife, I'm sure you've already read that report. And it will be difficult, for a long time, but it will get better and you have people around you that will help you"

Elizabeth nodded and Daniel smiled slightly.

"I better get these papers to Jack before he court-martials me."

Daniel headed out of the room when Elizabeth's voice stopped him.

"Thank you"

Daniel turned to her but she was already looking back down at the papers. Daniel sighed and left her office.

2 Months later

Daniel sat opposite Jack in his office; once again, he was worried about Elizabeth. Since his talk with her 2 months earlier he expected her to come and talk with him, it didn't happen. If anything, she'd isolated herself more and he knew it wasn't healthy.

"Jack, can't you just talk to her?"

Jack threw the mini basketball into the mini hoop, which was situation just next to the briefing room door before turning to Daniel.

"Danny, Elizabeth is a grown woman. If she thinks she can handle this she probably can. Anyway, you're closer to her than me; if you couldn't get through to her I doubt I can"

Daniel nodded

"Yes Jack, valid point but Elizabeth might need to talk to someone who doesn't know her so well; it might be the only way for her to open up."

Jack sat down and leaned over the desk

"Danny, I'm uncomfortable around pregnant women. Their hormones are everywhere; I mean I don't like to cross Elizabeth normally, but now…"

Jack shuddered and Daniel shook his head. Jack then got serious

"Danny, that woman has been to hell and back these last few months. What she really needs is our support. If she doesn't want to discuss it, don't push her."

Daniel smiled at Jack's soft side

"Jack, you have a soft side"

Jack smirked

"Don't tell Carter, but I like that woman. She can hold her own, I respect that."

Daniel smiled.

"Knew you liked her"

Jack smirked,

"I'll talk to her, if you really think it will do any good"

Daniel smiled at his triumph and left Jack's office.

Jack walked into Elizabeth's office and saw her sat at her desk, eating chocolate.

"Elizabeth, I thought you were suppose to be spending more time at home and less time here"

Elizabeth eyed him suspiciously.

"If you thought I was home why did you come to my office?"

Jack walked over to her desk and picked up a bit of the chocolate.

"I heard you had chocolate."

Elizabeth smiled

"What's the real reason Jack?"

Jack nervously leant on her desk and sighed, popping a piece of chocolate into his mouth.

"We're worried about you Elizabeth. You haven't seemed like yourself"

Elizabeth bit into another piece of chocolate and glared at Jack

"What makes you think I'm not like this all the time?"

Jack tried to pick up another piece of chocolate but she batted his hand away

"Elizabeth I've spoke to Rodney and Ford. They are worried about you. Elizabeth you need to talk to someone."

Elizabeth sighed

"If memory serves you've already made me talk to a psychologist."

Jack nodded

"And if memory serves you only met with Kate twice. I hardly call two, one hour sessions talking about a problem."

Elizabeth stood up slowly walked around her desk to Jack

"Jack, I am fine. I don't need to be coddled"

Jack placed his hands on her shoulders.

"Elizabeth, I am not coddling you. I'm worried about you"

"Jack…"

Elizabeth stopped and winced in pain. Her hand shot to her abdomen.

Jack placed his hands on her arms and held her steadily

"Elizabeth are you okay?"

Jack lead her over to the small couch

"Here lay down"

Elizabeth shook her head

"I'm okay, I'm okay"

Jack laid her down on the couch, went over to the desk and picked up the phone

"Infirmary, send Dr Beckett up to Weir's office"

Elizabeth's hand stayed on her abdomen as Jack walked back to her. He placed his hand on hers.

"How long have you been in pain?"

Elizabeth winced again.

"A few hours. I just…I'm afraid Jack. I don't know if I can do this alone"

Jack held her hand lightly

"You are not alone. You have so many people who are going to help you. You and your child are not going to be alone"

Elizabeth nodded slightly as Carson came into her office and walked over to her.

Jack stepped out of the way and Carson say down next to her on the couch.

He placed his hand on Elizabeth's abdomen and felt for the baby.

"How long have you been in pain?"

Elizabeth thought the question had come from Carson until she realised it wasn't his usual Scottish accent. It was an American accent. It wasn't Jack, it was John.

She looked to her side and saw John standing behind Carson. He smiled at her.

"It's time. I'll be here with you. I promise"

Elizabeth nodded slightly, knowing it was finally over.

She dropped her head and looked at Carson.

"I'm in labour Carson"

Carson looked up at her and nodded.

"I'd say so"

Carson and Jack helped Elizabeth to her feet and steadied her.

"Let's get you down to the infirmary"

Elizabeth gripped tightly onto Rodney's hand. Rodney became red and shouted out in pain

"Good damn it Elizabeth. Be gentle, my hands are delicate pieces of equipment."

Elizabeth glared at him, Aiden, sensing this was going to end worse for Rodney ushered him out of the way.

"Rodney why don't you go do something and I'll stay here with Dr Weir?"

Rodney looked at him hurt.

"I want to be here for her…"

Elizabeth cut him off

"…Rodney if you care for me, you'll go get me chocolate right now"

Rodney nodded and headed out of the infirmary.

Aiden grabbed Elizabeth's hand. He lightly squeezed it and smiled at her.

"You know you're going to be okay"

Elizabeth smiled and gently squeezed his hand back

"Thank you Aiden"

Another contraction hit her and she cried in pain trying to avoid hurting Aiden's hand.

The pain subsided as she felt a hand on her shoulder. She looked to her side and saw John standing there.

"You're doing fine. They can't see me, so we can't talk properly."

He bent down and kissed her forehead, sliding his fingers though her hair.

"This is going to happen quickly. Soon you're going to see our son"

Elizabeth nodded slyly as another contraction hit her.

Carson came to her and smiled

"I think we'll be meeting your child within the hour. This seems like a quick labour Elizabeth"

Elizabeth nodded slowly, tears forming in her eyes because she knew that as soon as her baby was born John would finally leave her.

John looked at her. He didn't want this, he didn't want to leave her but he had no choice. He'd made a decision with the Ancients.
He would be allowed to stay with Elizabeth for the duration of her pregnancy and after that he wouldn't be able to make contact with her again. He could watch over her but not make contact.
He'd done it to ensure his son's safety from all the dangers in the world and beyond. The Ancients hadn't been happy but John did have help from Oma and they eventually agreed but with a clause. If John left the Ancients, they would stop their protection on his child. They needed John and would do everything in their power to stop him leaving

John turned to her.

"Remember that night after we came back from P2X-455?"

Elizabeth nodded slowly.

"We went out to the balcony and looked at the stars. I held you in my arms and I kissed you for the first time. That was one of the happiest days of my life. And you're about to make me that happy again"

"Bloody hell"

Elizabeth cried in pain as the final contraction hit her.

She collapsed on the pillows behind her as she heard the small wail of a baby.
Elizabeth smiled and looked to John.
She watched as he started to fade away into the blinding light she'd seen before,

"He's beautiful Elizabeth, just like you. I love you and I love him. Make sure he knows that"

Elizabeth let the tears she'd been holding back fall as John finally disappeared.
Elizabeth closed her eyes as she felt something being put in her arms.
She opened her eyes and looked down at the small baby. One of his hands was waving at her while the other one was in his mouth being chewed on.

"You have a beautiful baby boy Elizabeth"

Elizabeth drew her finger down his cheek tenderly until he reached and grabbed her finger with his tiny little hand.
Elizabeth turned to Carson, Aiden and Rodney who had re-entered the room 15 minutes earlier

"Thank you for being here, but if you don't mind. I'd like a little time alone with him"

All three of them nodded

"Of course. He's so beautiful Elizabeth"

Elizabeth smiled at Aiden's comment as they left her alone. She placed a delicate kiss on his tiny head

"Hey, hey my sweet boy. Your daddy would be so proud of you. He's looking over you though, and he loves you so much. And so do I. You'll have everything you want and need. I'll protect you from anything. What do you think about the name Jonathan, in tribute to a great man?"

The baby gurgled and smiled at her.

"You like that name. How would you like to be called that?"

He gurgled again and Elizabeth smiled

"Jonathan Sheppard it is then"

A week later

Elizabeth walked from the kitchen with her son in her arms as she heard a knock on the door.

"Shall we go see who that is? Yeah"

She opened the door and was met with a big teddy bear, waving at her. Behind it, Jack smiled at her.

Elizabeth glared at him

"Are you trying to bribe my son?"

She moved away from the door and let him in. She closed the door and led Jack into the living room, placing Jonathan into a small cradle.

Jack placed the teddy bear onto an empty chair.

"And something for his mother"

He pulled a box of chocolates from behind his back.

Elizabeth smiled, took the chocolates and placed them on the desk.

"Thank you. You want a drink."

Jack shook his head.

Elizabeth ushered for him to sit down on the couch and Elizabeth sat next to him.

"What can I do for you Jack?"

Jack glared.

"I can't just see my favourite diplomat without having an agenda?"

Elizabeth nodded

"Come on Jack. Let's be straight."

Jack nodded and looked over at Jonathan.

"How are the two of you?"

Elizabeth smiled

"We'll be okay."

Jack smiled back at her before moving over to the crib and picking up Jonathan

"He was visiting you, wasn't he?"

Elizabeth lowered her head slightly

"How do you know?"

Jack sat back down and bounced Jonathan on his knee slightly.

"When Daniel was ascended he came back sometimes to guide us. You were so…private. I thought since the beginning, when you told us about when you saw him that he wouldn't leave so easily. When you told us you were pregnant. Well, I just knew…"

Elizabeth nodded and leant back.

"I always thought it would be easier after I'd had Jonathan. But it's not. I still need him"

She closed her eyes and let a few tears fall.

"He'll need his father. I'm not good at the whole male role-model thing."

Jack nodded

"You might not be, but he'll have lots of people looking out for him and most of them will be men. Me, Danny, Ford, Carson and Rodney, we are all here for you."

Elizabeth sat forward and nodded taking Jonathan from Jack's arms.

"I know. But it's not going to be the same"

Elizabeth was woken up later that night by crying coming from the room continued to hers, her son's room. She slid out of bed and began to walk over to the room when the crying stopped. Elizabeth was filled with a feeling of warmth. She walked into her son's room and stopped herself at the doorway, observing what was happening.

Around Jonathan's crib was a bright white light, but it didn't scare either of them, it calmed them. Slowly the white light began to form and it changed into that of a man. Into that of John's.

John slowly picked up his son, who was gurgling at him, obviously recognizing who he was.

"Hey, shhh. My little boy. I can't believe how much you look like your mother. But you got my hair. That'll drive your mother crazy, especially when it comes to class photographs."

She watched as John closed his eyes and placed a kiss on his son's head

"I love you kid. Always remember that. I'm glad I got to hold you. Even if I never get to do it again. I should go now. I love you"

Elizabeth watched as John disappeared into a white light with Jonathan still in his arms. The light gently guided Jonathan back into his cradle before disappearing through the roof.

Elizabeth smiled, tears filling her eyes.

They'd be okay.

Fin…