Spoilers: Um, Season 8 Gemini in a way but not too sure since I've never seen any of the episodes in full..
She is a shadow of herself.
Walking in the dark she finds herself alone despite the fact this ship is not empty. Her brethren surround her; they are her ship, her safety net.
But she isn't safe by far. Not from herself.
She's cut up inside, humanity missing somehow and yet unleashed in so many other ways – harrowed by her training.
She's what he wants and so he has her by his side. But she isn't Samantha Carter anymore; she's beyond the weakness's and limitations of such a fragile body. She's not yet perfect but he thinks so anyway, blinded by his love.
A love that her other self broke and that she suffers for each day.
He keeps her here because he can't let go – so childish, selfish and nowhere near logical – in there somewhere it's her punishment and that may be the only part that makes sense.
She's wiser than him, she knows the truth. Perhaps one day he'd see through his naivety, that to be superior you take all that is strong and rip from you anything that does not fit. That it hurts is a given; is why he can't stop loving and that's why he continues to be pathetic. Clinging to the fragments painfully rather than cleaning the wound and bleeding once again. It would be a short lived agony but he will not have it.
Once she felt something for him, a remnant of Carters sadness most likely, and this she felt today too even after she had tried to eradicate such weakness. The past is meaningless, only the future matters; all she wants from the past is knowledge. To learn, improve on what she is as he has taught her, but that is not the only reason. She wants to make them proud. She's not sure who they are anymore that she wished to impress, since it's a lingering feeling in her mind and they hardly matter if she no longer wanted to know who they were.
That feeling haunts her briefly, but she knows it has no place, just another flaw she's discovered. She might have cherished it if she was the original, except she flees from that tenderness, the warnings of human slights. That's the difference between them, the one he pretends not to see. Like her new version could exist cut off from her past and yet still be what he loved. That denial is futile but he uses it as if it is a protection. He can't see it won't do him any good, that it will be his downfall.
Fifth is her creator, something she may be, in the loose usage of the word, grateful for. Although she doubts he'll think that act so wise soon.
She mourned for him today, for all the hurt they had caused him between them.
But no more.
Why care for that mistake when you know the only actions you intend to take will cause the same reactions?
So she mourned him today, finally and only, before she ceased to care.