Stargate Atlantis: Betrayal

Notes: I do not own this show or any of the characters, the series is great at it is! Takes place after the events of Hot Zone.

Doctor Elizabeth Weir was fuming and extremely upset, she just couldn't believe how reckless he had being and how stupid it was of him. Even though she did have to admit if he hadn't gone against her orders that the city would have still been in lockdown but that was beside the point. Major John Sheppard had undermined her authority and that pissed her off beyond words, but for some reason it also wounded her deeply. After all this time, she would have hoped that he had enough respect for her to even hear her out but this didn't appear so. She had asked him earlier if he trusted her to which he had answered yes. But the real question was did he really trust her?

Weir furiously reached for her mug of tea and downed the contents in one go before turning back to the laptop open on her desk. More reports to go through and especially the ones Doctor Carson Beckett had been sending up concerning information on the virus that caused this entire situation. Then there were arrangements for the really deceased team members that the virus had claimed to deal with and for once, she hated her position as expedition leader. No matter how much she tried to set her mind to the task, she found herself taking no comfort in her work and Elizabeth couldn't concentrate long enough to finish it all. She decided she needed some air and left her office, crossing the control room to the outer doors where she stepped onto a beautiful balcony, the gentle ocean breeze a comfort.

Walking over to the rail, she leaned on it and closed her eyes. Allowing her mind to wander and her skin to feel the tingling and warm sensation of the sun and breathed evenly. As soon as she closed her eyes, she saw the look on Sergeant Bates' face and heard Sheppard's voice. Weir quickly opened them and a frown washed over her face. When she wouldn't open up the door to the gym where Sheppard and Teyla Emmagan were confined to, he had ordered to Bates to open up the doors and after some time he had carried it out. Weir would never forget the way she felt when Bates looked up to her and said, "Sorry Ma'am." It was the first time she realised what Colonel Sumner and General O'Neill had said about Sheppard was true. Deep down, Weir had always hoped that the man would prove them wrong. It would never happen again, she had told Sheppard.

"Yeah right," Weir muttered to herself and the vast ocean before her.

"Is this a private moment or can anyone join in?"

Surprised and startled, Elizabeth turned round and found herself face to face with him. "John," she said taking a moment to register. "No. I was just leaving," she said intending to walk past him and go back inside until he side stepped to the right and blocked her path. "Something you want?"

"Yeah actually." Sheppard paused a moment. "I just wanted to apologise once again for what happened earlier." He ran a hand through his hair, which always had that dishevelled look then put his hands on his hips.

"There's no need," Weir said shortly trying to get past him but he mirrored her every move each time.

"There is," Sheppard confessed. "Look I do feel bad about what I did, but I don't regret it. I did the right thing." Of that much, he was certain. Weir just looked up at him in silence. "And you know I did."

The look he gave her was so piercing and she felt as if he was looking right down into her soul and she didn't look away. "I won't dispute that John," Weir replied calmly. "It's just…"

"I undermined your authority and made you look incapable of running Atlantis in front of Bates and oh the whole control room?" Sheppard finished.

Weir wasn't about to admit that he had got it in a nutshell although Sheppard took her silence as a confession.

"Just for the record, I don't think that." That got her attention. "I know my opinion doesn't count," Sheppard carried on but it counted to Weir more than he would ever realise. "But I think you're handling this job extremely well but you know about me. You said yourself Sumner and General O'Neill warned you. I'm a man of instincts and that's what we need to live on out here."

Weir had never figured John Sheppard as a man of words but what he was saying, strangely to the diplomat, made sense. A lot of sense in fact, "So it's nothing to do with the fact that you don't think I can handle things?"

"Hell no," Sheppard answered, sounding more like the person she had grown to live with. "I mean there isn't exactly a guidebook on how to survive in another galaxy with a race of aliens who suck the life out of you. You're having to go with your own instincts in order to get the job done, so why can't I?"

What Weir wanted to say and actually say were two very different things. Inside she was thinking that Sheppard was saying the exact words that she had been longing to hear, he was right about having to live on instincts alone for out here. Basically, they were all they had in the fight against the Wraith.

"Next time you decide to pull a stunt like that, I'd appreciate it if you actually discussed it with me rather than going off half-cocked." Sheppard opened his mouth to argue until Weir carried on with a small smile. "Unless of course time is of the essence and you do actually have a point." This turnabout in behaviour seemed to shock Sheppard into silence and as Weir was figuring out. This was a hard task at the best of times but for now she would take what she could get.

"Well," Sheppard finally began with an own smile of his own. "I'm glad we had this discussion."

"Me too," Weir said putting her hands behind her back, it was good to get back on track and get any hard feelings out of the way. An awkward silence followed as the two of them regarded each other and the scenery surrounding them.

"I'll leave you to it," Sheppard said taking his hands off his hips and turning to leave, walking over to the doors. Weir watched him with a sad expression, she would have enjoyed his company around now but as usual, he was all about the retreating. As if sensing this, Sheppard turned back round and she forced herself to look at him brightly. "Goodnight Elizabeth."

"Goodnight John."

With that said and done, Sheppard disappeared through the door. She turned round and stared out at the city, at the beautiful crimson sky and the crystal blue ocean and Elizabeth Weir was left alone, once more.