The Yankee and Clarence go out to offer help to the wounded. The first one they find stabs the Yankee when he bends over to help him. The Yankee's wound is not serious. Merlin appears, disguised as a woman, and offers his services as a cook. The corpses begin to reek with disease, and Clarence and many others fall sick. Clarence awakes to find Merlin gesticulating over the Yankee's sleeping form. He declares he has cast a spell on the Yankee, which will make him sleep for thirteen centuries; in his glee, he runs against one of the fences and is electrocuted. Clarence and the boys hide the Yankee's body in the deep recesses of the cave and swear to write down if any of them escapes alive from their predicament and hide the manuscript with the Yankee. The manuscript ends there.
In the postscript, the narrator tells how he finishes the manuscript at dawn and goes to the stranger's room. He finds him in bed, delirious, calling for Sandy. He says he has had a terrible dream of a revolution and the death of the king and that he was a man of the future and was somehow sent back to his own time, separating him from his home and all he loved. He thinks he hears the king approaching and calls to lower the drawbridge, and then he dies.
Clarence adds the last chapter to the manuscript, as the Yankee cannot bring himself to record his stabbing by an ungrateful noble. Ultimately, the conquerors conquer themselves; technology's triumph over human opponents brings death to the victors from the ensuing decay, in a strangely post-apocalyptic scene. The people whose destiny the Yankee and the nobles came to this place to fight over are nowhere to be found; in the end, they had no role in determining the outcome either way. Merlin's spell presumably (and inexplicably, given his other failures) works, since the Yankee shows up to give his manuscript to the modern-day narrator. The book adheres to the laws of science in all instances except the episodes of time travel, which is brought about once by brute force and once by a magic spell.
Merlin's triumph recalls (and refutes) the Yankee's statement at the end of chapter 39, "Somehow, every time the magic of folderol tried conclusions with the magic of science, the magic of folderol got left." Merlin could be interpreted as a symbol of man's need to take refuge in a belief in illusion. Twain remarked in 1905 in a speech on Joan of Arc to the Society of Illustrators (in which he mentioned A Connecticut Yankee in King Arthur's Court) that "illusion is the only valuable thing" in the world. In the end, only the sixth century is real for the Yankee, and he has been separated for a second time from everything he holds dear. He dies in the midst of his last "effect."