Author: Vicky
Category: romance, angst, slight crossover in part 2 and beginning of part 3
Summary: John wants Elizabeth to meet someone
Season/Sequel: future season
Rating: PG-13 just in case but most of the time it shouldn't be more than G
Archives: my website, Command Dynamics, Atlantica, Abydos Gate: Fanfiction others ask please, I never refuse
Beta: csiangel
Disclaimer: I own neither the show nor the characters. I don't earn any money; I just do it for fun.
Author's Note: I have the idea of this fic while watching Allies, the season finale, though there's no spoilers in that fic. Names' meanings are taken from here. This is the longest fic I've written in English and the 2nd longest fic I've ever written. It took time, but it's finally there. So enjoy!
This fic is for my LJ friends 'cos they're fantastic people! tacklehugs everybody

Sweet Secret

Prologue

Propped up on an elbow, John was watching her sleep. It was the middle of the night and though he was tired, he didn't want to sleep yet, or he couldn't to be more precise. Thoughts were running in his mind and he couldn't shut them out. So he was observing her.

He loved doing that during the day, and he especially liked to see her blush every time she noticed she was under his scrutiny. But what he liked the most was observing her at night, when she was asleep next to him or in his arms. A few years ago, if someone had told him the womanizer that he was would settle with a woman like her, he wouldn't have believed them, nor would he have believed them if they told him that it would be happening in another galaxy. He knew he was lucky to be with her, and he wasn't ready to screw it up.

They already had their fair share of troubles when the IOA found out about them. It wasn't as if their relationship was forbidden by any regulations; even thought she was his superior, she wasn't in the military and nothing could stop them from dating, he had checked that one out personally. But they were still frowned upon by the IOA and under scrutiny from them. So far, they had both been professional and they couldn't do anything against them. But he knew that one day, they would screw something up and the Comitee would finally have a reason to fire one or both of them.

Right now, he hadn't the IOA in mind; actually, his thoughts were as far away from them as possible. He was thinking about the fact that in a few days time, they would be on Earth once more. Although during their first year they had all hoped to see Earth again, now it wasn't the same. He knew that a lot of them, Elizabeth and him included, didn't consider Earth as their homeworld anymore. Now, what they hope was that they could stay on Atlantis as long as they could.

But, at the moment, he was debating within himself, trying to find the courage within himself to tell her something he had in mind for quite some time now. It wasn't as if something was wrong; actually it could go wrong but he would have to tell her first. He just didn't know how. But he knew one thing: the more he waited, the more difficult it was going to be to admit it to her. If he was honest with her he was afraid that she could reproach him to not have told her sooner, say at their first meeting or when they started dating, but he had never really found the time. So really, it wasn't his entire fault.

Ok, who was he trying to kid, of course it was his fault. He really should have told her sooner. But it's not like he could go back in time and correct his error. No, they would have to deal with it. And maybe, just maybe she wouldn't be too angry with him the day he'll tell her about it, about his sweet secret.

Chapter 1

Elizabeth, John and some other members of the expedition were once again on Earth for their yearly detailed report, and for the selection of new members. Since Earth had acquired a ZPM, trips between Earth and the Atlantis base in the Pegasus Galaxy became more convenient, and the two senior members could afford a few days away from the SGC.

For their first real holiday together on Earth, John wanted Elizabeth to meet a special someone to him. Since their first date, he had wanted to tell her about this person but never found the right moment to do so. He didn't know how she would react but decided he had to take the risk; if Elizabeth found out even more lately, she might be angry at him that he hadn't told her sooner. So, taking the chance of a few days of freedom, they took a plane towards Atlanta, Georgia.

John stopped their rented car in front of a small house in the Atlanta suburbs. Turning towards Elizabeth, he took one of her hands in his and looked into her eyes. He didn't know what to say or what to do. He hoped he was doing the right thing by telling and showing Elizabeth the truth but he was unsure. He really wished that it wouldn't break their relationship; these last five months since they first began dating were the best ones he could remember since his childhood and he really hoped it wouldn't end like this. A few days before asking her to their first date, he realized he came to love her more than he loved any other woman. With her, he was ready for a lifetime commitment although this very idea was unimaginable with other women he dated.

Elizabeth could see he was nervous, and she was beginning to be a bit scared of what might happen since he had only told her he wanted her to meet someone. She remembered perfectly well the only other time she saw John this nervous. It was at the end of their first date; he had taken her on one of the mainland beaches for a picnic and when they stood up at the end, they were face to face and John was so nervous that she was the one who kissed him to reassure him.

Like that night on the beach, Elizabeth leaned towards her lover and kissed him lightly on the lips. It seemed to wake him from whatever state he was in and a small smile graced his lips. She brought her free hand to his cheek and he turned his head slightly, kissing her palm.

"Elizabeth… Before we go in there, I just want you to know that I'm sorry I haven't told you sooner."

"What is it, John? God, you're scaring me!"

"I'm sorry. I promise you, it's not a bad thing... At least, I think it's not. I just don't know how you'll react."

"Why don't you tell me, then?"

"I'd rather show you. Come on, let's go."

John left the car, quickly followed by Elizabeth. Hand in hand, they walked up the path to the house. Once in front of the door, he squeezed her hand one last time before knocking. A few noises were heard from inside, followed by footsteps before the door was cracked open.

Elizabeth saw no one at first but then, she lowered her gaze and noticed that the door was opened by a little girl. Elizabeth estimated she could be no more than five or six.

"Abby, how many times have I told you to not open the door yourself?" The young woman who came rushing behind the girl stopped when she saw the pair. "John!" she exclaimed, engulfing the said man in a hug.

Elizabeth couldn't help the pang of jealousy she felt seeing John being hugged by another woman, but she tried to reason with herself; John was with her and she couldn't doubt his feelings. Breaking the embrace, John bent over and picked up the girl, kissing her soundly on the cheek which made her giggle. He then seemed to be whispering something into her ear but Elizabeth couldn't catch the words. Another feeling took the place of the jealousy in her chest; now more than before she feared what he wanted to tell her.

Finally, John turned towards her, the little girl still in his arms.

"Abby, this is Elizabeth. Elizabeth, I want you to meet Abby, my daughter."

Elizabeth was left speechless by John's words; she had played a lot of scenarios in her head but, she never imagined that one.

"Elizabeth, you ok?" John enquired.

"Yeah… I'm sorry, I was… Hi Abby," she greeted the girl, who buried her head in her dad's neck, instead of replying.

"She's shy," he explained. "And this is Dinah, Abby's godmother and her mom's best friend and housemate."

"Nice to meet you, though I couldn't say that John talked about you."

"Likewise. Why don't you two come in?"

She gestured for them to enter and John directed them to the living-room. They sat on the couch, Abby on his lap, and Dinah settled down in an armchair. Elizabeth was still feeling uneasy and was waiting for the other shoe to drop. Looking at John's daughter, she noticed that she had his eyes and the same hair colour, though hers was not unruly like her father's. If someone had asked her opinion, she would have said that she didn't know what she inherited from her mother; Abby seemed to be a girlish mini-replica of John.

"By the way Dinah, where's Clare?"

Dinah's face became gloomy at John's question.

"I tried to reach you, I really tried, but I've never found you. Nobody knew where you were."

"What? What happened? Dinah?" he asked hastily, understanding that something bad had happened to his daughter's mother.

"She was in a car accident. A drunken driver hit her car. They said she… They said she died instantly."

"Oh my god...," John whispered.

He slightly tightened his grip on his daughter, keeping her close to him. Elizabeth closed her eyes, feeling sorrow for a woman she never knew, but who had a great place in the three other people's lives.

"When?" she heard him ask, before opening her eyes.

"Eight months ago. You never told us where you were. Listen, I don't blame you, I just wish I'd have been able to tell you sooner."

"I'm sorry. I know I should have left an address where you could have contacted me. I…"

"It's okay, John. I took care of everything."

"How did Abby react?"

"As well as she could. She understands that her mother will never come back. The first few weeks were difficult; she kept asking about Clare. She had nightmares too; she still has some from time to time. I've never taken her to the cemetery; I know it's her mom, but it's not a place for such young children in my opinion."

"You're right. Oh… Elizabeth, I'm sorry, I nearly forgot about you," he said, remembering her presence.

"It's okay. I understand," she said with a slight smile, taking one of his hands in hers. "So, uh… How old is Abby?" she asked, trying to change the conversation, for which John was grateful. "I'm guessing five, maybe six years old?"

"She just turned five last month. She'll start kindergarten in September."

"Since we're talking about this, I have something for you in the car, sweetie."

He stood up, settling Abby down on the couch, beside Elizabeth. He was leaving the lounge when his daughter's voice made him turn back to her.

"Daddy, stay."

"I'm coming back. I just have to go to the car outside. Stay with Elizabeth and Dinah, okay?"

"Okay," she replied, pouting.

"John, why don't you get yours and Elizabeth's bags also? You can stay in the guest room."

"Well, we were going to stay at the hotel…"

"You know you can stay here."

"Are you sure?"

"Yeah. Besides, I'm sure Abby doesn't want her father to leave her every night."

"Elizabeth?" he asked his companion.

"She's right. It would be better for Abby to have her dad with her."

John nodded and went out to retrieve their bags. Left alone with Abby and Dinah, Elizabeth was feeling even more nervous than before; the little girl never really acknowledged her presence. Dinah's voice broke her out of her thoughts:

"I know your mind must be full of questions, and I also know that you may not ask John for answers so, I'm going to tell you. John and Clare had never really been together. It was just a one night stand but it turned out that Clare got pregnant with Abby. She told him and he just took his responsibilities. John is a fantastic father with Abby; she's daddy's little girl and has him wrapped around her finger."

"I can imagine," Elizabeth said, smiling gratefully at the younger woman. "She looks so much like him!" she added, looking down at the girl sat beside her.

"Yeah. She definitely took after him which sometimes caused some problems…"

"Don't I know that!" she exclaimed, exchanging a knowing smile with Dinah.

"You and John work together? You're also in the USAF?"

"No, I'm a civilian and diplomat. And I happen to be John's boss so yeah, I know how much trouble he can cause sometimes."

"Excuse me if I'm indiscreet, I swear I'm too curious for my own good sometimes, but how long have you two been together?"

"It's okay. We've been together for a little more than five months."

"I'm back!" John said, closing the door behind him.

"Daddy!" Abby cried, jumping of the couch.

"Here," John said, kneeling in front of her. "It's for you kiddo. I've left the bags by the door," he said, standing up and turning to Dinah.

He went to sit back on the couch beside Elizabeth, sliding an arm across her waist and kissing her lightly. Meanwhile, Abby was sitting on the floor, ripping off the paper and opening the box containing John's present. She took what was in the box out and, Elizabeth's could see bird-shaped pieces of wood; she guessed that John had asked one of the Athosians on the mainland to make them for him.

"Wow, John, it's beautiful!" Dinah exclaimed seeing them.

"Yeah. Sweetie, I know it's not a toy but you could still play with them."

"Thank you, Daddy," she said and John leaned over so she could slide her arms around his neck, as she tried to stifle a yawn.

"I think it's time for your nap," Dinah said standing up.

"No, no, no" she replied shaking her head. "Wanna stay with Daddy."

"Nope, Dinah's right, you have to take your nap," John said standing up with Abby still in his arms, her eyes half-closed despite her protests. "I'll tuck you in, ok?"

When John came back a few minutes later, he could see that Dinah wanted to tell him something. Resuming his seat next to Elizabeth, he draped his left arm around her shoulders and turned towards his friend.

"What is it, Dinah? There's something more, isn't there?"

"Yeah. Shortly after Abby's birth, Clare went to see a lawyer to put down her will. She wanted to be sure that Abby would be taken care of if something happened. I didn't know about it; I found out at her death," she paused, knowing there's no good way of saying this. "She wanted you to take Abby, John."

"What?" he said, surprised.

"This was also why I tried to reach you, to tell you that."

"But, you're her best friend and Abby's godmother, why…?"

"And you're her father. Believe me when I tell you that I love Abby as if she was my own daughter, but Clare was right, she has to stay with you. A judge entrusted her with me for the time being, and you'll just need to sign some papers whatever way you choose."

Elizabeth was surprised by Dinah's revelation and she could say the same went for John; she had felt his grip on her shoulder tighten when he learned the news. She knew that thoughts were running in John's head but she didn't know what to do to help him; things considered she couldn't as much as she'd want to.

Dinah knew that the couple needed some time alone to process the news so she stood up and turned towards them.

"I'm sorry but I have to leave you alone for an hour or so. I have to do some shopping for tonight's dinner."

She left the room then the house, closing the door behind her.

Elizabeth didn't know what to do or say. She was still stunned by Abby's appearance in her life and if she was honest, maybe a little angry at John for not having told her sooner. Finding out that her companion had a daughter with another woman wasn't the idea Elizabeth had of this holiday. Nevertheless, a part of her understood why John kept it a secret until now. She doubted that anyone else knew about it and he simply wanted to keep it a secret as long as possible, even between them. Who knows, if they weren't together, she might have never known.

She was drawn out of her thoughts when John gently kissed her right temple. Turning towards him, she saw that he was worried and managed a small smile.

"Are you angry at me? I know I should have told you sooner, I know that, believe me, but…"

"It's ok, John, I understand. But yes, I have this feeling; I don't know what it is exactly, anger, or disappointment because you didn't trust me with this before."

"I'm sorry, I really am," he said the last part with his lips close to hers and then kissed her passionately, leaving both of them breathless.

"Why didn't you send them a message when Rodney managed to open a wormhole back to Earth?" she asked; this question was on her mind since she found out.

"What would I have said? 'Hey, it's Daddy, I'm not sure I'm gonna make it'? I would never have done that to them."

Elizabeth just nodded in response while John pulled her into a tight embrace.

"You ok?" he asked her, even though he knew her answer would be negative.

"I'm not sure, John. It was a lot to take on such a short notice."

"I know," he simply said as she broke up the hug and stood up. "Elizabeth?"

"I need to go for a walk. I need to think."

"Ok," he said, standing up himself. "I would have kept you company but…"

"You can't leave Abby by herself. Besides…, you have a lot of thinking to do too."

"I guess… Will you be ok? After all, you have never been here."

"I'll be fine, John," she reassured him, kissing him before opening the door. "And if I ever get lost, I'll call you."

"Be safe," he whispered to her as she crossed the threshold which made her turn back to him. "What?"

"Nothing. It's just that usually, it's the other way around."

Smiling at him, she turned around and resumed her walk down the path. John followed her with his eyes for a minute or two and then closed the door. He climbed up the stairs and opened the door to his daughter's room. Looking at her sleeping peacefully, he knew Elizabeth was right; he had decisions to make. He sat in the dark beside the little bed, silently praying to God to give him answers.

Meanwhile, Elizabeth was walking down the quiet streets, lost in her thoughts; someone could have called her, she wouldn't have heard them. The last two hours were probably the weirdest in her life. While she was feeling confident when they landed into Atlanta airport, now doubt filled her. She knew John had to make a decision about Abby and, she would never ask him to choose between her and his daughter. Deep down inside herself, she was really afraid to lose John for the first time. She knew that there was always a risk when he left for a mission but this time, it was different. If she was honest to herself, she already knew what John's choice would be; she saw it in his eyes. She just couldn't help but hope that she was mistaken.

She stopped while passing by a park. Children were playing under their parents watch, running or swinging, playing football or throwing a ball to their dog. This reminded her of her own dog, still waiting for her at Simon's. She didn't really want to see him but she also knew that she'd have to take Sedge back one day or another and thus face him. She knew that she was over with him, she had John now and she probably loved him more than she had ever loved Simon; maybe it was time to undo the last bond she had with him by getting her dog back.

Deciding to stay there for a moment, she sat on a bench beside a woman with a baby in her arms. Watching children play, she couldn't help but imagine Abby, John and her together. Even though she didn't know the little girl, she took a liking to her; maybe because she looked so much like John. She felt that Abby was distant but she hoped that whatever happened they could get to know each other. Maybe she was a little selfish here but she really wanted John's daughter to like her.

Turning her head towards the woman who shared the bench with her, she noticed that she was also looking at her and smiled in return.

"I'm sorry, I didn't want to stare but it's the first time I've seen you here. I'm Jess by the way and this," she said looking down at the baby in her arms, "is Michael."

"Elizabeth," she replied, shaking Jess's free hand.

"So, you're new in the neighbourhood?"

"No. I'm just here with my companion to see his daughter," she answered, hesitating slightly on the last word.

"You didn't know about her, huh?" Jess asked and she got her answer in Elizabeth's eyes before adding, shaking her head, "Men are such cowards, sometimes."

"No! Not John. He's not like that; actually, he's all the contrary usually. He just didn't know how to tell me."

"So, pardon my curiosity, but why aren't you with them?"

"I just needed to think about that for a while. It was a lot to take at the same time."

"I can imagine. Yesterday, there were just the two of you and now you're three."

"Yeah. It's kind of distressful. Oh, I'm sorry to bother you with my problems. We don't even know each other and…"

"Don't worry," Jess interrupted her, "I'm a mom at home with problems of her own and I know how good it is to vent at someone, and especially if you don't know them."

"In that way, thank you for having coped with me. I'd better go back now," she said standing up.

"Maybe we'll see each other again one day and I hope everything will turn out ok for you."

"Maybe… And thanks."

They bid their final goodbyes and Elizabeth began to retrace her steps towards the house. She was still dreading John's decision regarding his daughter but also knew that they'd work things out. Somehow, Jess managed to restore some of her confidence in their relationship.

Meanwhile, at the house, John was still watching Abby sleeping, lost in his own thoughts. And lost he was. He was still unsure of what to do; two options arose, each of them meaning that he had to give up on one of his two precious loves. Unbeknownst to him, Abby started to stir and opened her eyes.

"Daddy?" she asked in a sleepy voice.

"Hey, baby," murmured John, sitting on the bed and Abby put her head on his lap. "Why don't you sleep for a few more minutes?"

"No. I wanna play with you. Please…," she said with puppy-dog eyes.

"Ok. Let's hope that Dinah won't be angry at us for that. Come on," he added, standing up, with his daughter in his arms.

"I love you, daddy," Abby whispered in his ear, tightening her hold onto him.

"I love you too," he whispered back, now knowing what his choice would be.

When Elizabeth knocked on the door a few minutes later, nobody came to answer it. Not wanting to wake up Abby in case she was still sleeping, she tried the knob and the door opened. Straining her ears, she heard a faint sound coming from the backyard and headed towards it.

There, she saw John and Abby, playing football. She couldn't help but smirk at the sight of them. Father and daughter were so enthralled in their game that they neither saw, nor heard her. She let out a small giggle, shaking her head.

"You're already trying to corrupt her?"

"Come on, Elizabeth!" he exclaimed, not surprised by her presence and she realized that his military skills probably told him she was here from the first few seconds. "Football is the best sport in the world! You'll have to admit it one day!"

"I don't think so," she said, narrowing her eyes at him before turning towards Abby. "Do you like football?"

"It's okay," she answered shrugging her shoulders. "But I prefer dance."

"I'll tell you a secret," Elisabeth started, crouching in front of the little girl, "I prefer dance to football too."

"Hey, you two! Would you stop ganging up on me?"

"I don't think so…," she replied with a grin plastered on her face and she stood up and brushed her lips against John's.

"Daddy, I'm hungry."

"Ok, let's go inside and see if there's something to eat."

One arm around Elizabeth's waist and his other hand in his daughter's, John steered them towards the kitchen, making them sit at the counter while he checked the cupboards.

"Let's see what we have here… Anybody wants cocoa?" he asked turning around in time to see Abby nodding vehemently.

"I'll do it," Elizabeth said, standing up. "But you'll have to tell me how you want it, young lady."

"Ok."

Watching his two favourite girls, John held back a sigh. He really wished things could be this way every day, but he also knew it was impossible. Gazing up from what she was doing, Elizabeth caught his eyes and smiled at him.

Just as he was going to say something, the front door opened and a very familiar voice resounded.

"I'm back!"

"We're in the kitchen," John replied.

"Is it cocoa I'm smelling?" Dinah said, entering the room.

"Yeah, Abby and I are doing some. Would you like a cup?"

"Yes, thank you."

"I hope you bought some cookies 'cos there aren't any," John said, crossing his arms.

"Yes, John, I have them. Here, help me put away the groceries."

"Aw, Mom but I don't want to!" he whined.

"John, stop acting like a child around your daughter."

"Fine," he grumbled before turning to face Elizabeth and Abby who were giggling. "No giggling you two!"

A few minutes later, they were all sitting at the kitchen table, sipping on their cocoa and eating chocolate cookies. Once he saw that Elizabeth finished her cup, John took her hand and motioned at her to follow him outside.

They stood in the middle of the backyard in silence, both knowing why they were there but neither knowing what to say. Finally, John opened his mouth to speak only to be interrupted by Elizabeth's finger on his lips.

"It's ok. I know. I understood when I saw both of you playing. You're going to keep her and stay with her here."

"Yeah," John only whispered, not knowing what to add. "I'm sorry," he said after a moment.

"Don't be. Would I have been faced with this choice, I'd probably have made the same decision that you have. She needs you."

"And I need you too."

"I'll be there. Just not right there. It's not because you won't come back that we can't be together anymore, right?"

"Right. It would be a long distance relationship."

"A really long distance one," she said in a laugh before hugging him.

John slid his arms around her, keeping her close to him. He knew that he made the right choice for his daughter but it still hurt thinking that he wouldn't see Elizabeth everyday, that he couldn't protect her anymore.

Back in the kitchen, Dinah watched the couple from the window; she was feeling guilty for having imposed this choice on John. But she didn't have much choice herself; it was Clare's will.

"Dinah?" the little voice asked and she turned her hand towards her. "Why's daddy crying?"

Surprised, Dinah looked from Abby to John and she could actually see some tears making their way down from his eyes; to say she was shocked wouldn't be enough.

"I'm going to see him," Abby said before jumping down from the chair.

"No, stay here," the older woman replied, grabbing her arms. "Let them have some time together."

Outside, the couple was now kissing slowly, softly, murmuring words of love to each other.

That night, after having put his daughter to sleep, John came in the room he was sharing with Elizabeth to find her sitting on the edge of the bed, waiting for him. She stood up as he closed the door and locked it, silencing him by a chaste kiss. Putting her hands on his chest, she looked at him in the eyes and whispered.

"Make love to me, John," she begged him and he didn't need to be told twice.

That night, they made love slowly, as if it were the first time they saw the other's body. They fell asleep in each other arms, her head resting on his chest, just above his heart.

John woke up the next morning to see Elizabeth, already dressed, sitting on his side of the bed.

"Hey, sleepyhead."

"Hey, yourself," he replied before drawing her towards him for a morning kiss. "You're up early," he said, checking what time it was.

"I have a plane booked in three hours."

"What?" he cried out, shock evident in his voice.

"I'm going back to the base."

"Why?"

"Because it will be better. And I have to inform Generals Landry and O'Neill that you're not coming back; this way they could think about a replacement."

"Why don't you call them instead? I don't want you to go now."

"I don't want to but I have to, John. Please, understand my decision. I have to sort things out in my head."

"I guess I don't have much say in the matter anyway. You would be leaving whether I agree or not."

She just nodded and John could see she was on the verge of tears. He took her in his arms, holding onto her as if his life depended on it. They stayed like this for a long moment, neither of them wanting to let go but Elizabeth, knowing that the sooner would probably be the better, slowly broke the hug.

"I'm going to ask if I can bring Sedge back with me. This way, I'll still have someone to keep an eye on me."

"Yeah, you'll do that. Let me get dress and I'll drive you to the airport."

"It's ok, I've booked a taxi; it should be here in half an hour."

"Ok…"

Right on time, half an hour later, a taxi pulled up in front of the house. Elizabeth said her goodbye to Dinah and Abby while John took her bags and went with her outside. The taxi driver put them into the trunk and took back his place, waiting for her.

Once again, the two hugged tightly, sharing a few kisses before John rested his forehead on hers.

"I'll miss you."

"I'll miss you too. Write me from time to time, ok?"

"I promise. You better go or you're going to miss your flight. Not that I would mind," he added with a smirk, making her chuckle a bit.

"I love you."

"I love you too, Liz," he whispered back, using the nickname he gave her on their first date.

Pulling back from his arms, she got into the taxi and the driver drove off.

Watching the taxi go away, John, not for the first time, was wondering if he did make the right choice.

To be continued...