Mag's Contract
First off I love this movie, seen it countless times.
My question is why hadn't Mag paid off the contract on her eyes, I can roughly speculate that she had been working for Gene-co for about 17 years, before Shilo was born. She should have paid off the work by then allowing her to leave with her eyes.
Now if the whole reason was just an excuse to kill her and force Nathan to make a horrible choice of loyalties i'll accept it, but does anyone have any other thoughts?