What even is the point of Nezumi's memories of being sexually assaulted being fake? What even is this plot point? Why would you spend so many chapters of a manga establishing that she had been raped as a kid and how this affected her, only to later go "oh this was all fake", wtf.
It feels like the author is trying to make the organization less bad, which is really stupid. You really want me to believe that a crime organization would not be willing to use sexual assault to control people, but would rather just spend money paying scientists to brainwash little girls and traumatize them? Because that's somehow morally better?
It's just really stupid. Is this trying to make the readers more sympathetic towards the boss guy? You introduce him to the readers by showing him raping Nezumi and other little girls and then you go "None of that was real, he's actually nice!".