My father left what happened to your mother and family in my hands. I even remember what I told him. "She made us a lot of money and left us with a well running Game Corner. We'll have her business again when I have control over Johto anyway. When that time comes, I'd rather have her loyalty than rule her by fear."

[...Dad even ruffled his hair for that one...] Your mother knew too much about Team Rocket. Once you get involved, it becomes impossible to leave.