The boy in the container
Harry found Dexter as a small boy, sitting in his mother's blood inside a shipping container, and adopted him. Seeing the signs in the kid, he chose to teach him control: kill only the guilty and never get caught. He also hid from Dexter what happened that day. His lessons show up in flashbacks throughout the series.
The Code has clear rules: the target must be guilty, with proof, and Dexter has to learn to blend in, fake feelings and never leave a trace. Harry died years before S1, but his son still hears his voice with every choice.