Rorke hired you to make it easier to brainwash people. You were an excellent scientist and he knew that, so he used that to his advantage. He manipulated you into doing what he wanted, with a side of threats of death of course.

You did not want your skills being used to hurt people, you wanted to use your science to help people. But, you'd rather not be thrown into the river.

Logan was your first experiment. He spent a while in the pit, being tortured and being forced to eat poisoned berries. But he was adamant on not getting brainwashed. He fought back against all of that propaganda and refused to let Rorke get control, so you were forced to take action. Using your science to make a formula that would make him fall into place easily, but this was just an experiment to see if it'd work. It wasn't the final formula.

Logan sat on the floor of your lab, his wrists chained to the wall behind him and ankles bound together. He was always silent, but always had that angry look on his face.