Title: Mistake

Season: 3

Spoilers: Possible spoilers for everything up to season 3's episode "Sunday"

Pairing: John/Elizabeth

Credit: Byrthelm, for correcting my mistakes.

Disclaimer: I don't own Stargate: Atlantis or any of its characters. No profit was made from this work and none will be sought. This is for entertainment purposes only.

Elizabeth didn't know how or when that happened, but over the three years of acquaintance – or close friendship to be more precise – with John Sheppard, they had developed a special connection that always seemed to make them aware of the other's presence and it was this connection that made her look up from her tablet to see him approaching her office. One glance at the Colonel was enough for her to know that there was something wrong, but no matter how hard she tried, she couldn't think of anything that could be the reason for it. Yet, the way he was walking, the expression on his face, left no doubts that he was very unhappy about something, not to say angry.

She was truly taken aback, when in contrary to what he usually did upon entering, he didn't address her in any way. Normally, he would either greet her, make some sort of a teasing remark about her working habits or suggest she goes to the commissary with him – if he wouldn't bring food with him already, and then he would either sit on the chair in front of her desk, always the same one, or go straight to the couch and make himself comfortable. This time, however, there was none of that. He didn't acknowledge her in any way and instead of sitting down, he turned around and closed the usually open door. This raised her curiosity even higher, because it was very rarely that this door was closed; it happened only during private conversations.

Placing the tablet on her desk, she turned in her chair to fully face him and opened his lips to ask him what was wrong, but didn't manage to say anything before he cut her off.

"Is that true?" he asked, looking at her and it was now that she realized that his anger was actually directed at her. This realization caught her completely by surprise. Obviously, it wouldn't be the first time he was displeased with her decision or something she did, but she was even more confused because this time, she had no idea what she had done to deserve that.

"John…" she started, but he didn't let her finish. She doubted he even noticed that she wanted to say something, just made this slight pause to gather his thoughts.

"You know, I would have thought that after all that happened, after everything we have been through together and especially after Earth, I deserved something more than that" he spoke, his voice bitter, his eyes devoid of the usual playful sparkles, so unfamiliarly cold that she felt her stomach twist. "I would have thought that our brief time as a couple meant something to you. You actually claimed that it did and yet here you are, treating me like a piece of trash you can just discard at any given moment, without saying anything, too!"

Her eyes widened as she looked at him in disbelief, almost unable to recognize the man that was standing in front of her in that moment. She dared to believe that she was one of those people in Atlantis, who knew him best if she was not at the top of that list; she had seen him at his best and at his worst and she had no doubts there were still layers to John Sheppard that she hadn't discovered, yet, but she had never seen him act like this towards any member of the expedition. It was almost like being transported back in time to the day when the Genii tried to take over the city, the way he spoke and looked at her reminding her of how he acted towards Kolya that day, and she would have been lying if she said that it didn't scare her.

Once again, she started to wonder where all of this was coming from. Now, after hearing him mention the time on Earth with such emphasis, she had no doubt it had to be something personal, but she still couldn't understand it. It had been a few months since they returned to Atlantis, so what brought this up now? She was pretty sure that after a few fights, they had managed to put this argument behind them, even if he wasn't really happy with it. No matter how much she was trying to hide it, neither was she, but there was nothing she could do about this situation because a romantic relationship with someone working for her, her right hand at that, was completely out of question.

There were moments, when she was grateful for the memory of their time on Earth, but there was also times when she couldn't help regretting it. She knew that nobody, not even Carson and Rodney, knew of anything that transpired between the two of them. She was trying really hard to fight him, but John was stubbornly not letting her cut herself off from him and even though it was infuriating at times, she was pretty glad that he didn't give up his determination and didn't let her become a true hermit, dwelling on what she had lost.

During the brief time before she found an apartment and lived at the Stargate Command, he would spend more time with her than without, be it in her quarters or accompanying her to the commissary or on a trip to town. He went with her to see every single apartment she considered and later helped her move. At the time, she had thought that the sooner she would find her own place to live, the sooner she would manage to avoid spending so much time with him, but she was mistaken. The first time he dropped by with a visit was three days after she moved in, and she was pretty sure it took him that long only because he had accompanied SG-1 on their mission, as the team discovered a place they believed to be of Ancient origin and needed someone with the gene to get inside.

It seemed obvious that he had seen right through her plan to isolate herself from everyone she had got close to during the time in Pegasus. He was her only, but very frequent visitor, coming to her place every single day unless he was on a mission and she didn't even realize when they crossed the line in their relationship that they had established a long time ago. Every day John would bring a different movie to watch and it soon became a tradition they set to catch up on all the new movies they had missed during their time in the other galaxy, and they would sit on her couch, eating takeaway or drinking beer and discuss what was displayed on the screen. Neither of them seemed to be aware of that, but they were gradually getting closer, mentally and physically and it wasn't long before cuddling became something completely natural for them, at least until one evening, she found herself lying on her back with John hovering over her, his hands caressing the bare skin they had found upon slipping under her T-shirt, the movie completely forgotten while they were making out like a couple of teenagers.

She had no doubts that if she had known at the time that they would be back in Atlantis so soon afterwards, she would have never allowed any of this to happen, but it felt right at the time. Neither of them could deny that there had always been something deeper between them, and after their return to their home plant, anything that had been standing between them in the past, didn't matter anymore. On Earth, she wasn't his boss anymore; they were just a couple of friends, who also happened to be attracted to each other and they were completely free to explore their bond. Those six weeks were a time, when they could follow their hearts and simply be Elizabeth and John rather than Dr Weir and Colonel Sheppard, bound by rules, regulations and their own sense of propriety and responsibility. It was the time to feel and even though it was a relatively short time, she was pretty sure that during those weeks, she found out more private little details about John than she did during the whole two and a half years that she had known him beforehand.

She couldn't say that she wasn't fond of that time, but that didn't mean that she was willing to change the rules she went by as the leader of Atlantis. One of them was that she wouldn't date people, who were working under her – what applied to practically everyone in the city, and no matter how tempted she was, she didn't plan to change it upon their return. John, of course, wasn't really happy with it and was trying to convince her that it wouldn't change anything. She could see the point in his words; whether they were together or not, their feelings wouldn't just disappear, and deep in her heart she knew he was right, but she didn't give in. He didn't like it, but he understood that it was simply the way she was, a person with a very strong sense of propriety, and respected her too much not to let it go. Yet there he was now, throwing accusations at her and ones she completely couldn't understand.

"John" she spoke, trying to sound as firm as possible so that he wouldn't try to interrupt her this time. "Can you tell me what is this all about? You storm into my office and make a scene, obviously expecting explanation from me and at the same time, you give me absolutely no hint of what are you even talking about."

She was trying her best to stay calm; fighting with him was the last thing she wanted to do, but his attitude seemed to influence her own and she couldn't help sounding a bit more challenging and defensive than she intended to. It was not surprising that it only seemed to add fuel to the fire and she was pretty sure that if it wasn't for the awareness of where they were in the back of his mind, John wouldn't try to tame his anger the way he was doing it now.

"How about the fact that you dump me the moment we come back here, even though you claimed that you loved me and that we meant a lot to you, saying that you can't afford being in a relationship with another member of the expedition, you refuse to spend the day off with me because it is too close to going onto a date, and then I find out that half of the expedition has seen you on a date with some Mark guy, who…"

"Okay, John, enough. I get it" she interrupted, raising her hand to prevent him from saying more. She knew him well enough to be pretty certain that there was much more to come, that he was only beginning his rant but she wasn't able to listen to it anymore. He was immediately taken aback by the change in her voice, the defensiveness all gone and replaced with resignation.

She could feel her heart sink and her stomach twist, when she heard the mention of that rather memorable day off, but even more so when he mentioned Mike. Suddenly, it all seemed to make sense. She probably should have thought about it, it seemed pretty obvious now, but she was sure that he didn't know about that particular detail. She hoped he was not going to find out, mainly because she knew that he would be very quick to jump to conclusions, no matter what the truth actually was. And the truth was that she wished she had never agreed to go to that lunch and felt absolutely terrible at the thought of that kiss, even if it was Mike, who initiated it and who himself admitted that he shouldn't have done it. She might have ended her relationship with John, but it still felt as if she was cheating on him and she truly regretted that she had given in that day.

Resting her elbows on the desk, she raised her hands to her face and massaged her temples with her fingertips, feeling a headache coming. She really wished she could explain her actions to him, give him any reason that would justify her actions, so contrary to the words she had spoken to him all those weeks ago. There was nothing, however. There was nothing she could say that would make him understand and calm him down when she believed that he had every right to be angry at her, especially when she was angry at herself, too.

His earlier words were echoing in her head and she felt as if he stabbed her right in her heart. She honestly couldn't blame him of accusing her that she didn't care, that she was playing with his feelings but the thought that he could really think that about her hurt terribly. Their time together on Earth might have been brief but she would have thought that even in those few short weeks, she managed to show him just how important he was to her. Even now, in Atlantis, she was pretty sure that her feelings for him were obvious, a little too much even at times, especially when he would get in yet another trouble during what was supposed to be just a routine mission.

"'Lizbeth..? You okay?" he spoke again, when she failed to say anything for a longer moment.

He was somewhat surprised by her lack of response. This silence seemed so completely unlike her that he started to wonder if she was actually feeling fine. When she told him to stop talking, he truly expected that she would snap right back at him, give him a lecture that would make him feel like an idiot for coming to her office and acting like a child or at least try to show him her way of thinking and when she failed to say anything, he started to worry. She looked okay before he came, but he knew her well and he could see pretty much every sign of a headache in her now, one that he was pretty sure was caused by nothing else but himself.

"I'm not" she eventually said, her words followed by a heavy sigh when she looked up at him again. "You are right, it was wrong of me to do all that but it has never been my intention to make you feel as if you, we, didn't matter. I meant every single word I spoke to you, John. I feel sick every time I watch you step through the Stargate because I know that this might be just the one time that you will run out of luck and not come back to me. I feel like dying every time you fail to check in of one of your team members dials the gate and informs us that you've got yourself into yet another dangerous situation. It has been like this for a long time now and it is not going to change, just like I'm not going to suddenly turn my feelings off."

"Then why, 'Lizbeth?" he asked, his voice now lacking its earlier venom. He was still angry, yes, but he just wanted to understand. "I can respect the fact that you don't want to be in a relationship with anyone from the expedition. Hell, you wouldn't be the woman that I came to admire if you didn't decide to follow this code of yours, even if I may not agree with your reasoning. Whether you like that or not, we are involved and just because we are not together doesn't mean that it isn't here. If anything, it only makes me long more for the closeness that we had back on Earth but that's not the point. You claimed that you love me, and then I find out about that scientist..! And it's not even you I find out about it from! Do you have any idea how that makes me feel?"

"Probably almost as bad as it makes me feel" she responded, lowering her gaze to her hands, which were now resting on the surface of her desk and which she was fidgeting with. "I will be the first person to admit that it should never have happened, and I wish I could say that he was bothering me so much that I gave in for the sake of getting some peace. I told him that I wasn't interested in any involvement with a fellow expedition member, and he immediately assured that it would be a lunch between colleagues, but even an idiot would know that he said that only to make me go. I honestly don't know what I was thinking, John and you have every right to be angry with me, to hate me even, I just hope…"

"God, Liz, I don't hate you" he quickly stated, being the one who interrupted her this time. "I'm pissed, yes, I feel betrayed and disappointed, definitely, but I don't hate you. I don't think I ever could."

When she looked up, she noticed honesty reflected in his eyes, along with so many feelings that it only made her feel worse. He might have had quite a reputation as a womanizer, an earned one too, but in this moment, everything she had thought about was confirmed. It was just a mask that the true John Sheppard was hiding behind, the caring guy she had found him to be and this was how she was repaying him for letting her in, letting her see the real him.

She opened her lips, apologies on the tip of her tongue even though she knew that it would hardly be enough, when the knock on the door reminded her of where they were. It was the sort of conversation they should have had in a more private place than her office, a room adjacent to probably the busiest place in the city where everyone could see them and who knows, maybe even heard Sheppard's raised voice. She glanced to her left and saw Rodney, his tablet in his hands, the expression on his face telling her that it was urgent and he wasn't going to go away before he talked to her about whatever matter brought him there. She looked back to John for a moment, hoping that her eyes would be able to convey her apologies, her guilt and regret as well as hope that one day, he would be able to forgive her. Then, she waved her hand, indicating for Rodney to come in and didn't fail to notice the confusion written all over the man's face when he stepped inside, looking between the two of them.

"What did you do again?" he asked John a few seconds later, earning a deadly glare from the Colonel.

"Nothing" he spat and then looked at Elizabeth. "I'll see you later" was everything he said before he walked out and she felt a twinge in her heart again.

"What did I do?" asked McKay, looking at her even more taken aback and she shook her head.

"Nothing, Rodney, it's my fault. Just leave him be. What is it that brought you here?"

She found herself surprised that he didn't continue the subject, almost never capable of reading between the lines and realizing when someone simply didn't want to talk about something, but she didn't appreciate it any less. Her gaze shifted to the control room for another second, resting on John's receding figure before he walked out of her sight, but she didn't have time to dwell on what had just happened. She didn't have time to be Elizabeth now, she needed to be Dr Weir and try to listen and understand what the scientist in front of her was telling her. She would have time to think about John and their conversation later, when she would go back to her quarters and retire for the night. Right now, however, she could only hope that she didn't destroy them for good.