The captain of the crew of Serenity is Malcolm `` Mal '' Reynolds ( Nathan Fillion ) . The episode `` Serenity '' shows that the captain and his first mate Zoe Washburne ( Gina Torres ) are veteran `` Browncoats '' of the civil war . The captain of the crew of Serenity is Malcolm `` Mal '' Reynolds ( Nathan Fillion ) and the episode `` Serenity '' establishes that the captain and his first mate Zoe Washburne ( Gina Torres ) are veteran `` Browncoats '' of the Unification War , a failed attempt by the outlying worlds to resist the Alliance 's assertion of control .