Complex sentence: Cain killed Abel and the original Elhaym to silence them, though the murder plagued his conscience and because of it he developed a guilt-driven sympathy for normal surface dwelling Humans, in effect breaking free of his programming to a degree.
Split into simpler sentences: Cain killed Abel and the original Elly to silence them; however, the murder plagued his conscience. Consequently, he developed a guilt-driven sympathy for normal surface dwelling Humans, in effect breaking free of his programming to a degree.