The Commander of Atlantis

Hello all. Haven't posted in a while but I have been working on a couple of stories. This one is for Devilish Me who asked for something when Sam was in Atlantis and Jack comes to visit. Well here it is. It is 6 chapters and is finished so I hope to post regularly. Hope you all enjoy. As always I own nothing, and I suppose this is a little AU but don't let that stop you reading.

Colonel Samantha Carter wasn't used to this feeling, this feeling of complete and absolute panic. It was, however, totally warranted. Her life was about to be turned upside down and not in a very good way. She stood on the balcony of her quarters and looked out over the city that she commanded.

After almost a year in Atlantis, Sam was still enjoying her life here. Even though it was far from Earth, she was among friends. In fact, after her last two uncomfortable years at the SGC when she'd tried her best to avoid a certain someone, Atlantis was almost a dream position.

But yesterday that dream had turned into a nightmare.

The latest shipment had arrived from Earth and with it came a message about an inspection. Normally, Sam wouldn't worry. Sure, she'd spend time dotting the i's and crossing the t's, but she wouldn't be in a panic like she was now. And the reason for this out-of-character behaviour? The inspecting officer – Major General Jack O'Neill. Crap!

Sam hadn't seen her former commanding officer for almost a year, not since Daniel had been captured by the Ori and turned into a prior and General O'Neill had returned to the SGC to help rescue him. Seeing him then after such a long time had been strained to say the least. They'd both been very professional when on the job but there'd been none of the usual camaraderie she'd felt before that night!

Although he'd popped in to the SGC on occasion since going to Washington, Sam hadn't been alone with the General since the night she'd left his beloved cabin almost three years ago now, after they'd defeated Anubis. Not since the night they'd kissed, the night when she'd almost said yes to joining him in his room. Sam had been so tempted to just give in but she'd said no. She'd told him that it wasn't him it was her, and that they weren't meant to be. That was the night when she'd broken his heart and for that she would never forgive herself. Of course, she hadn't been allowed to see that. He'd always been good at hiding his emotions.

They'd had the row to end all rows and she'd left the cabin, taken Daniel's car to the local airport, and flown back to Colorado, where she'd requested reassignment to Nevada. When Daniel and Teal'c had returned to the SGC, they'd rung to tell her that the General had taken the promotion in D.C., effective immediately. He'd put his house on the market and sold his truck – all from the other side of the country. He'd been virtually non-contactable since then.

So, nearly three years had now passed since that night. Sam had thought a lot about her decision, especially when stuck in a lab in Nevada, or on a lonely night in another galaxy. And now he was coming here. She wasn't supposed to know but Daniel had slipped a note into the supplies. He'd thought, very wisely, that while she wouldn't bat an eyelid at an inspection, she'd freak if Jack were to walk through the gate unannounced. He'd also written that he and Teal'c would accompany Jack, just to keep the peace.

Although Atlantis came under Jack's command, he'd only visited once over the last couple of years, when he'd had his head sucked by replicators. Sam wondered why, when there'd been several other inspections carried out during the past couple of years, he'd only now decided to come himself. The professional officer part of her knew he'd have to keep his hand in, be kept up to date with the goings on here, but the other part of her wondered if there could be another reason. Maybe he actually wanted to see her? But she squashed that idea quickly. If it was going to be a pleasant reunion Daniel wouldn't be volunteering to play chaperone.

Sam noticed the lights of Atlantis click seamlessly from their low night-time setting to a daytime one and she knew that the day was about to begin, a day that could be the worst one of her command here. She stood up straight, squared her shoulders, and prepared herself to meet whatever the day brought.

Sam wandered from her quarters through the deserted corridors to the commissary to pick up some fruit for breakfast. She nodded to the few night staff she passed on the way who were finishing their shifts and walked in to the smell of breakfast. Her stomach then decided that would be the perfect moment to make itself known. She paled and ran to the nearest ladies room and was quickly followed by the Atlantis doctor, Jennifer, and Teyla, who'd both seen her hasty exit.

The two women found Sam behind a toilet door, dry heaving. Jennifer, ever in doctor mode, took control of the situation. "Colonel? Are you okay?"

There was silence then, once the retching had stopped, Sam feebly responded, "Fine... thanks."

"I do not believe she is telling the truth," Teyla stated.

Jennifer nodded in agreement. "Colonel, I'd like to examine you. Please come to the infirmary."

Sam knew from all her time in the military that she was powerless to resist a doctor who wanted to prod and poke her, so she stood gingerly and flicked the lock on the door. She must have looked pretty awful because the two women's expressions turned to a mixture of worry and pity. She washed her hands and took a small sip of water from the bottle of water Jennifer handed her and allowed herself to be led from the room. She knew there was nothing wrong with her, nothing that a freak power overload disabling the gate couldn't fix, anyway.

Once in the infirmary Jennifer instructed her to sit on one of the beds and began to question her about the symptoms she was experiencing. "Is this the first time you've vomited today?"

"Yes," Sam responded weakly.

"Did you feel ill when you woke up?"

"No," Sam answered this time, not totally accurately but she certainly hadn't felt the need to throw up when she'd gotten out of bed. She also ignored the 'woke up' part as she hadn't really slept but didn't want to get into that.

Jennifer looked carefully at Sam before asking tentatively, "Is there a chance you could be pregnant?" The symptom of rushing to get rid of your stomach contents when smelling food first thing in the morning was very common in that situation.

Sam almost laughed but then came close to tears, answering quietly, "No, never a chance of that," much to the shock of the doctor. Jennifer looked slightly startled at Sam's emotional reaction but didn't push for any more information on that topic.

"Okay, just let me do some blood work to rule out strange alien diseases then you can go back to work."

"Oh, goody," Sam mumbled under her breath as Jennifer bustled around her. Just what she needed, a chance to go back to work and think about the inspection that was about to happen, which she wasn't supposed to know about, which no one else knew about, and which was being conducted by her ex-boss/person she loved more than anything in the world, or the universe, for that matter.

Fabulous.

AN: So there is chapter 1. Please review if you have time, they make me happy, but there is no obligation. Also try not to flame, that makes me sad. Chapter 2 very soon.