David Wilson, a young lawyer, moves to town, and a clever remark of his is misunderstood, which causes locals to brand him a "pudd'nhead" (nitwit).

His hobby of collecting fingerprints does not raise his standing in the eyes of the townsfolk, who consider him to be eccentric and do not frequent his law practice.

"Pudd'nhead" Wilson is left in the background as the focus shifts to the slave Roxy, her son, and the family they serve.

After fellow slaves are caught stealing and are nearly sold "down the river" to a master in the Deep South, Roxy fears for her son and herself.

She considers killing her boy and herself but decides to switch Chambers and Tom in their cribs to give her son a life of freedom and privilege.

Desperate for money, Tom robs and murders his wealthy uncle, and the blame falls wrongly on one of the Italians.

In a courtroom scene, the whole mystery is solved when Wilson demonstrates, through fingerprints, that Tom is both the murderer and not the true Driscoll heir.

Mark Twain's satire humorously and pointedly lambastes everything from small-town politics and religious beliefs to slavery and racism.

The first part of the book seems to satirize racism in antebellum Missouri by exposing the fragility of the dividing line between white and black.

The new Tom Driscoll is accepted by a family with high Virginian ancestry as its own, and he grows up to be corrupt, self-interested, and distasteful.

The circumstances of the denouement, however, possessed in its time great novelty, for fingerprinting had not then come into official use in crime detection in the United States.

In his early years, he has an intense hate for Chambers, although the other boy protects Tom and saves his life on numerous occasions.

Tom attends Yale University for two years and returns to Dawson's Landing with "Eastern polish", which results in the locals disliking him more.

Luigi and Angelo Capello, a set of near-identical twins, appear in Dawson's Landing in reply to an ad placed by Aunt Patsy, who is looking for a boarder.

During the writing process, however, Twain realized that secondary characters such as Pudd'nhead Wilson, Roxy, and Tom Driscoll were taking a more central role in the story.

This left the original team in, but only as mere names, not as characters.The characters of Luigi and Angelo remain in Pudd'nhead Wilson, as twins with separate bodies.

Twain was not thorough in his separation of the twins, and there are hints in the final version of their conjoined origin, such as the fact that they were their parents' "only child", they sleep together, they play piano together, and they had an early career as sideshow performers.

"Those Extraordinary Twins" was published as a short story, with glosses inserted into the text where the narrative was either unfinished or would have duplicated parts of Pudd'nhead Wilson.