Five days later, Mr Clark was at the docks. He had left the house and now he was watching their ship leave to the United States without him or his family. When the ship disappeared in the horizon, he stood up and went back home, crying.
I don't understand why it is not "had disappeared" because we can imagine the scene: Mr Clark was sitting and watching the ship leave for the USA, then once the ship had totally disappeared and the action of watching was completed he stood up . Even if the events are in chronological order would it better to use past perfect to emphasize the disappearance and of course the sadness of Mr Clark.