Author's Note- I promised myself I was going to wait on this till I got to it in the 'Missing Links' series but after a brief conversation about that kiss on GW I just couldn't let it go. Enjoy!

In His Heart

Jack O'Neill groaned out loud. It had been days since the kiss between him and Dr. Samantha Carter and things between him and his 2IC had been increasingly awkward.

He understood why it was awkward in a sense. He had kissed Major Samantha Carter's counterpart, a woman who in most sense of the word, was herself. But in that reality Dr. Carter had been married to her Jack.

Jack could have stopped her when she leaned up to him, she gave him enough time. But he hadn't wanted to. Not when a Samantha Carter was right there about to kiss him, how was he supposed to pull away?

Jack got up off his seat in the commissary and decided that he had to clear things up with his 2IC, or he was going to lose it.

*****

Jack found her in the spot that she was always at. Her lab.

"Hey." He said as he shoved his hands in his pockets.

Sam jumped at the sound of his voice. "Sir! Sorry, I didn't know you were in here."

"Listen…I think we need to clear a few things up." He said awkwardly.

Sam visibly stiffened at what he said.

"About that kiss…" He started to say.

Sam interrupted him. "I don't need to know anything."

"Carter, I know that was awkward with you right there to see. And I'm sorry." Jack said.

"You don't have to apologize for kissing someone sir." She whispered.

"Her husband had just died…and I looked just like him…I couldn't exactly tell her no." Jack said.

*****

"I know." She said not meeting his eyes. She would have wanted one last chance to say goodbye to her husband if she could as well.

But he had kissed her right in front of her. And it had been a blow. To have her CO kiss an alternate version of herself…it hurt.

She wasn't exactly sure why it had hurt so much, but it did. It could have easily been her there, kissing him.

It also showed her what she could have had, if things were different. If she wasn't in the Air Force, if Jack hadn't been her CO.

Sam's gaze traveled up to her CO's ruffable hair. She had to admit, he was a very attractive man. With his brown eyes that sparkled every time he laughed. And that grin that could melt her into a puddle. But she really loved his hair. It had slowly started to turn gray the past few years and Sam knew it suited him. And it was always ruffled, and she wondered what it would like to run her fingers through her hair. Her counterpart had. Would it be baby soft or would it be rough to the touch?

Sam mentally shook her head to clear her thoughts. Those weren't things that she should be thinking about.

"It was just a kiss." Jack whispered.

Sam felt a pang in her heart. To him it may have been a kiss, but to her it was what could have been. And he had willingly kissed the other Sam back. What she wouldn't have done to trade places with Dr. Carter for that second.

"I understand sir." And Sam flashed him one of her fake smiles.

*****

"It wasn't the same…it wasn't y…" Jack stopped when he realized what he was about to say. It wasn't you. That wasn't really something he could tell her.

Sam looked at him confused. "It wasn't what?" Sam asked.

"Nothing. It doesn't matter." Jack said hoping she wouldn't question him.

"Okay." She said slowly.

"I couldn't just leave her like that…she needed to say goodbye." Jack shrugged.

Sam smiled at him, the first one she had sent him in days and Jack felt relief.

"Are we good Carter?"

"Yes sir" She said.

Jack's mind wondered to the other Sam. She had fallen in love with her Jack. Could this Sam possibly ever feel like that to him as well? No, he figured she wasn't the type that would fall for a guy like him. She was a scientist and she only saw him as a friend, as her CO. As the man who's duty it was to watch her six when they were off world. And then there were the regulations.

Jack wouldn't fully admit it, but he knew that although his main reason for kissing the other Sam was so she could have one last goodbye with the man that was very similar to her husband. But he had also kissed her because he had wanted to kiss his Sam. But even he knew that she wasn't his Sam. No, his Sam was the one who had watched the kiss. She should have been the one he was kissing, she was after all the one who was very quickly starting to claim what little remained of his heart.

Jack glanced at her face and his eyes suddenly dropped to her lips. What would they taste like? He wondered. Would they taste like the cotton candy lip gloss that he knew she had on, or would they taste like the blue Jell-O that she always had around this time every day? What would it feel like to have her lips beneath his? Would she kiss him back or would she pull away? Would they be soft and yielding or when they be fierce? Would there be sparks or would it be as if he'd just kissed anyone? Would she kiss him back with the same intensity that he knew he'd kiss her with? He knew given the opportunity, (which he knew he never would have) he'd take her in his arms and kiss her with all these emotions that the Dr. Carter had brought to the surface.

Sam's voice startled him out of his train of thought and he quickly lifted his eyes back to hers. "Do you need anything else Colonel?" She asked.

"Ah! No…I'll just..." He said indicating the door. Jack sent her on of his grins. "Don't work too late." He said over his shoulder as he walked out.

"It's already late!" She said at his retreating back and Jack chuckled.

Dr. Carter may be a Samantha Carter, and for all he knew there could be hundreds of them out there, but she hadn't been his.

The woman who had his heart, probably had no idea that she had claim to it, but nevertheless it was hers. There was only one Major Samantha Carter and in the deep recesses of his heart, the places deep within him that he never thought about, he knew she would always be his. She'd be right there, in his heart till he drew his last breathe.

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Author's Note- Thanks for reading and as always if you liked it let me know!