Enterprising Lack of Intelligence

If I were creating a Star Fleet, one of the required Academy courses would be to look at the plots of a wide range of science fiction novels and develop processes to mitigate about those situations.

If the captain of the starship was subtly affected by alien mind-control, there'd be a pretty clear set of actions for dealing with that.

Actually, there'd probably also be an interesting set of "crying wolf" situations, too. People would use the "aliens have mind-controlled the captain" claim when it wasn't true. That'd be an interesting story.