From the beginning, the narrator emphasizes the frailty of human life by discussing his declining health, describing himself as "now but a shadow," although he "was a hale, hearty man two short years ago." The story is filled with mentions of sickness and death. The central plot focuses on the failed effort to transport the body of the narrator's friend, John B. Hackett, from Ohio to Wisconsin for burial.

Throughout this journey, the narrator has several discussions with Thompson, the train's expressman, who contemplates the certainty of death, saying twice, "we've all got to go, they ain't no getting around it." Later, after they mistakenly identify a box of guns topped with Limburger cheese as Hackett's body, Thompson catches a strong smell of the cheese. Feeling nauseated, he declares, "I'm a-dying; gimme the road!" and rushes outside to the train's platform for fresh air.

While Thompson does not succumb to the cheese's odor, the prolonged exposure to the cold winter air on the platform—due to their efforts to escape the smell—ultimately results in the narrator's death two years later. He remarks, "This is my last trip; I am on my way home to die." Although Thompson's fate is not clearly outlined, his comments while they endure the freezing conditions suggest a similar fate for both. He observes, "It's our last trip, you can make up your mind to it. Typhoid fever is what's going to come of this."

In the narrative, Twain explores how human imagination can overpower logic, leading to dire results. Early in the story, the narrator notes how Thompson "closed his window down tight, and then went bustling around, here and there and yonder, setting things to rights." Thompson is entirely focused on making the train car airtight, taking great care to ensure the express car remains warm for both himself and the narrator.

However, once they catch a whiff of the cheese, which their imaginations convince them is the scent of a corpse, Thompson "scrambled to his feet and broke a pane and stretched his nose out at it a moment or two." This not only negates all his previous efforts but also seems irrational. Given that Twain notes Thompson had closed the window, he could simply reopen it for fresh air. Regardless, in the panic caused by believing the smell is from a decaying body, he breaks the window. The narrator's imagination is even more powerful; despite knowing his friend has only been dead for a day, he never questions why the smell is intensifying. "By this time the fragrance—if you may call it a fragrance—was just about suffocating, as near as you can come at it."

Imagination continues to mislead both men. Neither questions the package of cheese on top of the white-pine box, even though the narrator earlier mentioned its location. Even when Thompson slips and lands "with his nose on the cheese," where the smell is distinctly stronger, he doesn't think to examine the package. In the end, the narrator reflects that after realizing the "smelly corpse" was actually a gunbox with cheese on top, "the news was too late to save me; imagination had done its work, and my health was permanently shattered."

Twain explores the theme of properly burying the dead. When Thompson inquires about how long the narrator's friend has been deceased, the narrator lies, saying "Two or three days" to explain the odor. However, Thompson doubts this and responds, "Two or three years, you mean." The narrator notes that Thompson "expressed his opinions at great length on the folly of delaying burials," ultimately stating, "’Twould 'a' ben a dum sight better, all around, if they'd started him along last summer."