You know the drill by now: all I own is an over-active imagination.
Spoilers for Season 4 of Stargate Atlantis.
Posting this here as it takes place on Atlantis, but in many ways it's an SG-1 story.
You'll have to read it to find out why.

The Chicken Or The Egg?

"Excuse me, Colonel." Sheppard knocked on the office door, "Can I speak to you for a moment?"

"Of course, come in." Carter motioned him towards an empty chair, "How can I help you?"

"It's kind of complicated." Sheppard closed the door and slipped somewhat hesitantly into the seat, "It's somewhat personal, and under normal circumstances I wouldn't dream of even asking this, but as it could affect everyone in the city, I feel I have to." He took a deep breath, "Did you get married before or after you found out you were pregnant?"

There was a moment of pure silence as Carter's eyes went wide with shock, then she sent a mouthful of hot coffee clear across her desk, forcing Sheppard to dodge out of the way. She coughed a few times, trying to stop herself from chocking, before looking up.

"What makes you think I'm either married or pregnant?" She asked, trying to regain her composure.

"Well, I've known you're married since you first arrived." Sheppard fidgeted in his seat, "You had a tan, but there were two white lines on your ring finger, a sign that you'd been wearing an engagement and wedding ring when you'd gotten it, but had since taken them off. It's not so noticeable now your tan's faded, but still..."

"How very, observant of you." Carter admitted, drumming her fingers on the desk anxiously, "How many others know?"

"Well I haven't told anyone, if that's what you're asking." Sheppard sounded positively defensive, "And I've not heard anything on the grapevine, so I think that secret is safe, at least for now." He sucked a breath in through gritted teeth, "But I'm not the only one who's noticed that you seem to be a little, uneasy first thing, and that you've started drinking decaf."

"Well, congratulations, Colonel; a deduction worthy of Sherlock Holmes himself." Carter sat back, letting the built up stress pour out of her, "I'm about two mouth's gone, but I can't be sure as I've not gone to see Dr Keller yet..."

"Because the moment you do, it'll be added to your medical file and transmitted back to Earth in the next data-burst." Sheppard nodded, "And you don't want the IOA to know, because they'll relive you of command and assign someone else."

"Yes."

"And does the General know?"

"And why would I tell him?" Carter asked, almost too quickly.

"Because he's the father." Sheppard smiled warmly, "Look, I've been around the Stargate program long enough to pick up on the vibe between the two of you, and you wouldn't believe the amount of money that's been building up in the betting pool on when the two of you are going to get together..."

"$22,357.47, at the last count." Cater smirked when she saw the surprised look on his face, "Cassie told me; she's been their unofficial inside source for years. We agreed we'd split it when it hit $25,000."

"Damn!" Sheppard looked somewhat deflated, "Wonder if its too late to get my fifty-bucks back?"

"I somehow doubt it." Carter relaxed, "And to answer your original question, no; I did not know I was pregnant when we got married, I'm not even sure if I was. And yes, Jack O'Neill is now my husband and the father."

"Well, then I guess it's you who deserve the congratulations." Sheppard's face lit-up with a wide-grin, "The only thing I can't understand is why you have kept it all such a big secret?"

"The IOA know that we're married, and understand that we wanted to keep it a secret for both personal and security reasons: we've made a lot of enemy's over the years, both on Earth and elsewhere. Can you imagine what someone like Ba'al would do if he found out?" An involuntary shiver ran down Carter's spine, "As for the pregnancy? I've reached a point in my life when it's now or never; I'd put my carer ahead of my personal life for so long that I honestly thought that I'd waited too long, that I'd never be able to have a child of my own. Don't get me wrong; I love Cassie as if she was my own, but still..."

"Just not the same?"

"No, no it isn't."

"So, have you told him?"

"No, and I suppose I really should; if you've worked it out, it's only a matter of time before someone else does, and then the IOA is bound to find out." Carter frowned, "And I doubt Jack would be too happy to find out he's going to be a father again through an official memo."

"Do you think there's going to be any repercussions?" Sheppard asked, "Officially?"

"Well, the IOA is probably going to want me to stand down as head of the expedition, if not immediately then soon. And Jack's going to want to be with me, either here or on Earth, so one of us is going to have to at least take a leave of absence."

"Well, I'm not going to tell anyone; I just needed to know, in case anything happened to you."

"I know, and I should have confided in you sooner." Carter stood, "I'll go see Keller this afternoon, make it official, then send a message though to Jack, asking him to set up a secure like so I can tell him face to face, even if it is over a video-link."

"Well, good luck." Sheppard got up to leave, "And if you need help with anything, just let me know."

The End