This is the worst twist in the history of twists.
The only reason it's a twist is because most protags don't have a realistic process of grief about finding out that their loved one is capable of committing atrocities for the hell of it, ending with acceptance.
Because, like, she was about to kill a huge amount of people. The only reason she didn't was because the protag stopped seeing her as a victim and stopped her.
Building up a shady secret organization for nothing is bullshit though.