Like many American films of the time, The Mystery Ship was subject to cuts by city and state film censorship boards. For example, the Chicago Board of Censors required, in Chapter 1, cuts of three gambling scenes; in Chapter 2, the slugging of the man and throwing him overboard; in Chapter 5, striking a man on the head with a stone, the mob inside of a wall shooting a man, and the man falling after the shooting; in Chapter 6, the abduction of the young woman in an automobile and the assault on the man; in Chapter 8, the gangster choking man on the ship deck, two scenes of man threatening young woman with gun, Chinese man threatening woman with dagger, Chinese man pouting poison on food, two closeups of young woman choking Chinese woman after she gains consciousness, one distant choking scene, and the last scene in the reel showing dagger descending towards the young woman; in Chapter 9, Reel 1, three closeups of Chinese man threatening young woman with dagger, man prying window open and entering house, Reel 2, man drugging cotton and placing it in telephone receiver, all scenes of man in torture chair, five fight scenes, putting unconscious young woman in automobile, threatening man with poker, and slugging man at garden gate; in Chapter 10, the last two torture scenes and the intertitle "You'll never leave us alive" etc.; in Chapter 13, Reel 1, the attack on young woman including her gagging and binding, entire incident of men shooting at each other from behind barricade of rugs and curtains to include men falling, Reel 2, the intertitile "She go die now", first scene of Chinese man chaining young woman to platform and all torture scenes where flames are shown except the one where she is rescued, gun shooting through opening in wall and two scenes of Chinese man falling, man aiming gun at prisoner, and shooting from trap door; in Chapter 14, Reel 1, chloroforming man by Man of Mystery and all but the first and last struggle scenes between man and young woman; in Chapter 15, Reel 1, foreign spy slugging agent, Reel 2, flash flogging scene, three scenes of choking man with rope, all scenes of man on young woman's bed after he takes false whiskers off; in Chapter 16, Reel 1, scene of young woman and man in bed, scene of Gaston pulling man from bed, man covering face with hands, young woman in bed covering face with hands, young woman turning away from man and burying face in pillow, and, Reel 2, binding of young woman; in Chapter 17, all but the last holdup scene, the two intertitles "You mean our wife" and "The one that gets the Queen of Hearts—gets the lady", three scenes of shooting at police, all scenes of playing cards for young woman up to time she awakens, three scenes of gang on bank shooting at police, two scenes of men shooting each other in cellar, three scenes of gang shooting at Mystery Ship; and, in Chapter 18, Reel 2, shooting from door and shooting inside shed.
