The story is just like what Kisuke has expected.
A branch family of Naberius House is researching something forbidden and they coincidentally got hold of a very rare member of nekomata lineage, a nekoshou, there are even two of them. It's precisely Kuroka and Shirone, who is now known as Koneko Toujou of the Gremory House.
The master of the branch family and his aide took great care of both of them for the next few days until they offered a way for Kuroka to become strong. But they were shocked that she refused and said that she only needs her sister's safety, which was Kuroka's biggest mistake.
They used the reason that Kuroka needs the power to protect Shirone in this dangerous world and she reluctantly accepted. At first, they only did some tests and exercises to gauge her natural abilities, but as time goes on, they slowly escalated to the point that she has to endure some physical traumas. This is all fine as Kuroka can see that Shirone is having a peaceful and fulfilling time and would always spend time to play with her. She also never told Shirone and abuses she's receiving as she truly believes that time that it is getting stronger.
It all changed when they started administering drugs on Kuroka after a few months of 'training'. Kuroka didn't feel anything in the first few sessions aside from her Demonic Power rising slightly even without her doing anything. Her opinion was changed, however, when they suddenly instructed her to lay down on a metallic bed and strapped her on it very securely. When the new drug entered her system, she felt unbearable pain that was akin to someone repeatedly stabbing her all over her body. Kuroka shouted and struggled wildly but she only noticed a smile from the master and his aide. It was then she realized that her good times end here.
That day, Kuroka returned to her's and Shirone's room but she ignored Shirone who is waiting for her and anticipating their playtime. She went directly to her bed and cried herself to sleep. Since that day, she stopped playing with Shirone, not because she didn't want to, but because of the lingering pain after each session being too horrible that it is unbearable to move even a little. Kuroka didn't want to let Shirone know her sufferings as she didn't want to worry her and Shirone might even confront the master which isn't very good in their current position.
Kuroka naively believes that all of this would end one day and keep on enduring. Her power visibly skyrocketed, but she learned how to downplay her abilities when they tested her. She did this because every time they knew her abilities improve and reached a certain point, they'll switch to a stronger drug. However, Kuroka couldn't hide her abilities forever as they would strangely switch their attention to Shirone which gives her a bad feeling. She thought that if she doesn't improve, they would the same thing to Shirone.
This would continue for a few more months and the relationship between Kuroka and Shirone became awkward. They still cared about each other, but they rarely talk now. Shirone is just a small child, so she was just throwing a tantrum.
On the fated day that Kuroka killed the master and his aide, they injected a drug to Kuroka so strong that it slowly melts her body and resulted in a pain which she hadn't experienced before. She already built up some resistance to incredible pain, but the pain of the last drug just puts a test on her willpower and vitality. The effects of the drugs subsided after a few hours but it left her life hanging on the thread and she pretended to sleep to rest a bit but still have awareness of her surroundings.
The master and his aide really thought that she's asleep due to her apparent weakness, so they started talking about their plans without moving to their usual heavily guarded room.
Kuroka overheard them and was shocked at the contents of their talks. The master thought that Kuroka is already reaching her limit, but their research is far from over. The aide then suggested disposing of Kuroka and using her little sister as her substitute to continue their research.
Those words are the last straw that broke the camel's back. She didn't care about her wellbeing and didn't react much from being disposed of, but the safety of her little sister, Shirone, is on the line and she couldn't imagine her sister suffering the same pain she did in the hands of both of them. Without thinking about the consequences, and incredible power welled up from her inside despite her almost dying body and manage to overpower the High-Class Devil and his aide, killing them. But not until they were able to call their reinforcement.
The power that propelled her already disappeared and she has to escape with Shirone. But she stopped and think again, is it okay to bring Shirone with her? She didn't do anything, it was her crime and bringing Shirone with her will just make her an accomplice. If they're caught, Shirone would die with her. With an answer in her mind, Kuroka escaped alone with her failing body.
Fortune would be on her side as she was able to escape alive and also heal somewhat. But the same blessing didn't apply for her little sister as she was captured as a suspect and was immediately put into death row.
She panicked and didn't know what to do and was about to rush to her execution site to save her even if she dies trying to. That's where she coincidentally met Sirzechs and Grayfia who are also going to attend the execution as the representative of the Devil Kings.
Kuroka tearfully beg for their mercy and told them the whole story. But like any normal people, they wouldn't easily believe the account of one person especially on something as ridiculous as this case so they set a ceremony to read all her memories to confirm everything she experienced. After the ceremony, both Sirzechs and Grayfia were convinced but although they can help Shirone and take her in, they can't prove Kuroka's innocence as they have no physical evidence. A memory reading ceremony was already banned a century ago and if others were to know he used it, his political opponents can take advantage of this point and attack him.
They first saved Shirone from execution and immediately went to the branch family of Naberius Clan to investigate and gather evidence but they were already too late as the scene was already cleared up.
Sirzechs didn't have a choice but to let the little Kuroka escape after healing all of her injuries as the higher-ups already put a bounty on her head. If there is no evidence to back him up, she won't be able to save Kuroka as saving Shirone who has done nothing to aide her sister killing their master his limit.
"And that's how the SS-Class wanted criminal Kuroka came to be. I don't know where she is now as there is no news of her ever since." Sirzechs finished his narration.
Rias is clenching her fist while Akeno is covering her mouth with her hand after hearing all of it.
"Why!? Why didn't tell me all about this!?" Rias raised her quivering voice.
Sirzechs expression didn't change and answered her simply, "Because you don't need to know about it. There's nothing you can do."
"B-But--"
"And it'll only put you and Koneko in danger. You might even do something stupid as confronting the Naberius House." Sirzechs didn't let her finish her sentence.
"..." Rias wasn't able to say anything about that as she's really thinking of doing so.
"Haah..." Sirzechs heave a sigh and faced Kisuke who's still smiling at him, "Good day, Urahara Kisuke. This is the first time we meet. I'm Sirzechs Lucifer, the Devil King who's in charge of domestic affairs.
"Good day to you too. Urahara Kisuke, a shop keeper."
"..." Sirzechs didn't know how to react to that so he just chooses to ask what he wants, "How did you know about Koneko's history?"
"I didn't know of it. It's just my speculation that her older sister didn't really lose control like they're told."
"Hooh... So you found evidence?"
"Hahaha... I wonder if that's a piece of evidence, but it's not on me right now and I can't give it to you." Kisuke replied with a laugh and thought, 'That evidence may prove useful to me in the future, no way I'm going to give it to you. And I don't really know about this Kuroka to help her. I only promised Koneko-chan to let her meet her.'