A/N: And voila – my next story. Completely unrelated to the Sweetest Sin. The sequel (that I started writing first) is still giving me a hard time, but I do promise to post it as soon as it gets itself organized in my head.

This one is angsty – in a different way to my last one – please bear with me. I have the first two chapters completed, and have roughed out the third…

Please R&R and let me know what you think – this is a harder one to write.

Disclaimer: Not mine. Sadly. Hey… do you think they'd sell 'em to me?

The Choice Ch1

She just wasn't herself lately. Hadn't been for a long while, and he had no idea what to do for her. No more happy-go-lucky science Sam. Just some sort of shell.

In the weeks prior, she seemed to be in some sort of pain. When he questioned her about it, she would just brush him off, and tell him it was nothing for him to worry about. But he still caught her grimaces.

She had been going to the infirmary a bit more than usual, but due to doctor patient confidentiality, Janet was able to keep whatever was affecting his 2IC behind closed doors.

Because it (apparently) hadn't been caused off world on a mission, and didn't stop her from being able to do her work, Jack didn't have to be made aware of what was going on. And that bothered him, because there was clearly something wrong with her, and all he wanted to do was help.

When they were off world she always stayed the good soldier - was aware of her surroundings, and any imminent threats. She stayed alert in briefings and acted like she was interested in what was being said – but when it was her turn to speak, there was less passion behind her explanations. And the big one - when it came to working in her lab, team nights and their occasional get-togethers in the commissary she just didn't seem to be there anymore; didn't seem to have the same drive as she used to. Like something inside of her had died. And he was worried.

(flashback to two months earlier)

Janet came into the room with an extremely sad expression on her face.

"Sam honey, I'm so sorry."

"What is it Jan?"

"We've finally got your results back, and it doesn't look good."

Tears started to gather in Sam's eyes. She needed to know what was wrong, but at the same time, didn't want to hear it. Like 'out of sight, out of mind' – if she didn't know what was causing the problems, then perhaps they would just disappear.

"Jan?" she prompted

"It's endometriosis Sam. And it's pretty bad. And Jolinar didn't help matters much. Her presence in your system would have eventually caused it to heal, however she wasn't there long enough, and what little she did start to repair, became even more out of control once she was dead, as she hadn't fully started the healing process; not to mention the presence of Naquadah that now remains in your blood stream."

"What does this mean? Aren't there things you can do? I mean, it's just mis-placed scar tissue, right? There are operations to scrape it out… aren't there? Anything…" her voice trailed off, as the enormity of what Janet was telling her started to sink in.

"That type of surgery, in this case, would only help a tiny bit. There's just too much of it, and it's all over the inside of your abdomen. The only real 'cure' for you would be a hysterectomy."

The tears really started flowing then. From both Sam and Janet.

"What about kids?" She barely whispered

If you want even the slightest chance – and it would be extremely slight – you would need to start trying now. And that's if the Naquadah doesn't get in the way. Best case scenario, you could conceive within one year. After that time period it will most likely be too late, and you would need the surgery."

Janet gave her a big hug, and Sam just let loose all of her grief into her friends shoulder.

(end flashback)

She felt dead inside. Now that she knew how unlikely she was to conceive, she realized how much she really wanted to have children – how much she always had. She just hadn't wanted them now – not at this time in her life.

She was finally living her dream – after working to get to the top in the StarGate program, she was finally venturing through the portal on a regular basis, rewriting scientific theories, and making other new and wonderful discoveries along the way. She was experiencing things that others could only come up with in their imaginations.

And her team; she loved them. If she left now to have a child, where would that leave SG-1? They'd probably find a replacement. But when she returned from mat leave, she would most likely be kept in the labs, or reassigned. There was no guarantee with the Air Force that if you held a job prior to mat leave, it would be yours when you returned.

Then there was the question of who to have children with. She and Jonas had discussed it, but he was dead now, and anyways, she couldn't imagine going to him with this request – or having kids with him. There was always in-vitro, sperm donors. But to be honest, that was a cold way of going about having a baby – and she'd be left to raise it on her own, when the time came.

To be realistic, there was only one man in this world she could imagine having a child with, and it could never happen.

So she'd just cut her losses. She'd rather have Jack's friendship, be able to work with him side by side, and keep her team/family together as opposed to losing them for a baby.

She cried herself to sleep that night, and every night for a good long time after that heart wrenching decision.

A/N 2: This is an idea I had after reading a story on another site.

I know that many people's experiences with Endometriosis are different, so if any of you have heard of or experienced different things with it, please forgive the way my story goes. One of my very good friends has Endometriosis, and was told she couldn't conceive, only to find herself pregnant with twins two years later (after refusing any surgery or treatment). So it is possible, and please keep this in mind as you read.

Also, please accept my Jolinar explanation. I'm going to stay on the thought process that she really wasn't in Sam long enough to heal her…

Cheers :)