When Chief Bromden sees McMurphy's lobotomy scars at the end of this movie, he realizes that the hospital has made McMurphy into an obedient zombie for life. It's the biggest bummer of the whole movie. Why? Because the scars mark the final victory of rules and conformity over freedom and the individual, which Chief expresses when he says, "Oh no. I'm not going without you, Mac."

That's why Chief decides to kill McMurphy. In his mind, this is the only way to give Mac back his freedom.

McMurphy has become a hero to the other patients in the ward because of his ability to stand up to Nurse Ratched. The others would be devastated to see Mac wandering around with dead eyes and a scarred forehead. So Chief decides to take matter into his own hands and to give Mac back his freedom, saying "I wouldn't leave you here this way" and smothering him. Then Chief gives freedom to himself by breaking out of the hospital and running off into the forest.