Huh. I feel like I missed something, because the story seemed fairly straightfoward to me.
The MC is an experienced assassin, who will happily kill men, but steadfastly refuses to kill women. Regardless of her reasoning, she seems blithely ignorant of the lives she destroys and harm she inflicts, beyond her direct targets.
After her last mission, her employer has gotten fed up with her BS and hired another assassin to go after her. This new assassin was related to at least one of her prior victims and got into the business for a chance at revenge.
She confronted the MC in the parking garage and only one because of the MCs refusal to kill women. However, rather than immediately kill her, she decided to humiliate her first, hence the rape. Somewhere along the way, she decided killing herself, and letting the MC deal with a dead woman on her conscience would be a better form of revenge, so that's what she did.
Finally, the MC hunts down and kills her old employer, but when confronted with his daughter crying over his body she aims her gun at the girl's head, rather than walk away.