David is the key
It seems that David’s behavior and actions in the films explain the reason why the Engineers wanted to kill humanity and what was “wrong” with humans in the eyes of the engineers. David can’t accept his imperfections which is what drives him to kill Walter. Also David being a creation by humans becomes more intelligent and wiser than humans and thus a threat to them just as humans become wiser and more intelligent than the engineers become a threat to their engineer creators.
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