Alright, I'll ask some questions then.
Would the Ketsurui perform this specific experiment to create these two specialized soldiers, when they already have all of the other Neko? I honestly don't know and hope someone who has been here longer can clarify if that sounds reasonable. The part about killing a general and several squads of soldiers as a test run also doesn't sound quite right.
I am fine with her being a specialized Neko, but becoming an "emotionless being of pure death" is pushing it for me. I also can't tell if she's supposed to be a cold loner sniper or a charismatic leader. I think if you could focus on her being trained/designed as an assassin and then transitioning into a leadership role after the war when she was asked to train others, that would seem more natural. Meeting her love during that time helps explain the transformation as well.
I don't like the somewhat over the top story of heroism in the middle. It seems heavily borrowed from a certain movie, which itself was referencing other movies and other soldiers. It's not a dealbreaker, but I would feel more comfortable if it was deemphasized somewhat.
I actually like the idea of her losing someone important to her and retiring for a while to recover, but I'm not so comfortable with her seeming to become entirely unhinged during that time. Down to having a bunch of swords named after her. It's a little creepy, and I would prefer it be toned down and less melodramatic. One twist that might help the story be even more sad, and tie into her leaving SA for a while, would be for Minagi's more recent backups to have been lost or accidentally destroyed. I don't think a Neko would make it two years or more without any backup at all, but having her brought back from before she met Yumi would be a way to twist the knife while staying a bit more plausible.
Eventually finding herself and deciding to return to service is fine. Do you have permission from
@Dragonnova to use her character, though?
On the skills, there's again a weird back and forth from being trained to be a cool sniper and also somehow being created to be very empathic and a master of psychological interrogation and seduction. Again, I think it would be better to simplify her early life as a soldier who lightened up and gained leadership qualities later. If you want you specify that they *tried* to implant her with natural skills for gaining information and leading, but her early lack of personality caused this to backfire, then those instincts came to the surface once she had a few years of proper interaction and firsthand experience with people? I could go for that.
Hope this doesn't seem too nitpicky, I just see an interesting, complicated character in there, and it feels like you're trying a little too hard to make her 'cool' at times. Tone it down a bit, and the base you've built is pretty great. I hope you understand what I'm trying to say.