The narrator did not have a private room aboard the train. He was traveling in the baggage car with a big box which he presumed to contain the body of his best friend John B. Hackett. According to railroad rules and regulations, a corpse being transported by train had to be "in charge of and accompanied by a competent person." The narrator thought he was accompanying the corpse from Cleveland, Ohio to his friend's family home in Bethlehem, Wisconsin, but through a mixup at the station in Cleveland, a similar box containing a shipment of rifles had gotten substituted for the box containing the corpse. A weak point in Mark Twain's story is that someone left a package of ripe Limburger cheese on top of the box with the rifles. Presumably this cheese was being shipped somewhere along the same railroad line. The narrator and the expressman in charge of the baggage car both mistook the strong smell of the cheese for the smell of the decaying corpse inside the box--or inside a coffin which was enclosed inside a pine box, in accordance with railroad regulations. Because of the intense cold, the expressman had not only closed up every window and vent in the car but "now went poking around his car, stopping up whatever stray cracks he could find, remarking that it didn't make any difference what kind of a night it was outside, he calculated to make us comfortable, anyway." The reader is supposedly amused by the situation these two men find themselves in. The smell inside the baggage car becomes intolerable, but the weather outside is deadly cold. Everything they do to try to mask the smell only adds to it and makes it worse.
This story now seems pointless and contrived, but it is a good example of Mark Twain's humor and of American humor in general in his time. The dialect spoken by the expressman is the best part of the story. Most Americans lived on farms and in small towns in those days and had simpler tastes.