The boys- vought understood that Homelander would be an extremely powerful supe(even more so than soldier boy) and if he rebelled against them they couldn’t stop him. So they pulled “the world’s greatest psychologists” and decided it would be best to turn John’s mind into a broken jigsaw puzzle dependent on love and affection to control him. He later kills the scientists, almost ruins the company like 3 times, and nearly led the world to extinction.
Elfen lied- the scientists and crazed family leading the experiments wanted to use diclonius to take over the world so they decided to experiment and control them for their own means despite needing them to overthrow humanity. Lucy and her kind paint the facility red escaping, “bobble head pop” the remaining scientists, destroy the facility/island, and nearly destroyed the human race.