It's about time
Everybody thought she should be happy. She was good looking, intelligent, self confident and successful in her job, and almost everybody liked her. Well, that was true for her soldier/scientist persona but "private" Sam was another matter. How could she know about things most women took for granted? After the death of her mother there had been no other female around. She did not have many friends at school because she was too intelligent for most people to like being around her. The rift between her father and brother left her rather alone and looking after herself. And after joining the Air Force she was mostly surrounded by males.
She was really glad that changed at the SGC when she met Janet. She was a really good friend and liked to talk to Sam from one woman to another. Sam could talk to her about things she couldn't tell her teammates. Like what happened with the Shavadai or everything after Jolinar. How she was suddenly different than before with feelings and memories that weren't her own.
Nevertheless there were things she couldn't even tell Janet, like her feelings for her CO. She didn't know where or when it had started, and it wasn't that she had woken up one day and thought: "I'm in love with Jack O'Neill." No, her feelings for him had grown over the years. At the beginning so subtly, that she didn't even register it herself. While going onto missions together, she had to learn to know him, and so she watched him -and over him- as any good 2IC would do. She learned to read him and his body language. She learned to trust him and his instincts. Well, she learned to trust Daniel and Teal'c too, but with O'Neill it was different, almost like an instinct.
It sure didn't hurt that he was nice to look at and that she liked his shrewd kind of humor. Even if his big mouth got them into trouble with the Goa'uld again and again -he just didn't know when to shut up. But he was the kind of person that managed to inspire a fierce loyalty from his team and fellow soldiers. Add to that his motto, "No one gets left behind", and it wasn't so hard to understand why not only his team but everybody at the SGC came to his rescue and SG-1's without a second thought, if asked.
And there was the Zatarc incident. Suddenly she knew for certain that her feelings weren't one-sided, that he had feelings for her too! She was happy and devastated at the same time. Happy, because she shared his feelings, but devastated because she knew that nothing could come out of it -or, it rather wasn't allowed to come out of it. So they left it "in the room" - and for a long time, it worked. But the feeling of loneliness and discontentment in her grew and grew unti, suddenly, she thought she had figured it out.
She had some thinking to do. The following week, while on the Prometheus, she would take the time to think about her future. Perhaps it was time for a change...
TBC