In pre-Civil War Missouri, near St. Petersburg, the vagabond child Huckleberry Finn describes the events by which he and Tom Sawyer had discovered a fortune. Huck has been adopted by the Widow Douglas and her spinster sister Miss Watson, and his guardians, Judge Thatcher, Huck's best friend Tom Sawyer, and practically the entire town inform Huck that he needs to learn to read and write and read the Bible if he ever hopes to go to Heaven ("Do Ya Wanna Go To Heaven?"). The only one who doesn't attempt to pass judgment on Huck is Miss Watson's slave, Jim, who predicts that he will lead a life of "considerable trouble and considerable joy". Exasperated with the constraints on his daily life, Huck escapes his bedtime and steals away to Tom Sawyer's "hideout", an old cave. In the cave, Tom, Huck and a group of their friends plan to form a band of robbers who will rampage around the countryside ("The Boys").
Huck, on his way home, thinks about the confines of his life and his wish that he will find meaning in his life. ("Waitin' For the Light To Shine") Huck returns home in the darkness to find his Pap, a violent drunk, waiting for him, who drags him off to his cabin in the woods. In his drunkenness, Pap swings from tomfoolery to extreme violence as he rails against a government that would take his son (and his son's money) away from him ("Guv'ment"). Pap attempts to kill Huck, hallucinating that he is the Angel of Death, but passes out in an inebriated mess. The next day Pap goes off to trade and Huck takes the opportunity to escape. He kills a pig and scatters the blood and gore around the cabin in an effort to make it appear as if he's been murdered. Huck reflects that this is just the sort of thing Tom Sawyer would do, and Tom appears to sing a vaudeville-style turn about the usefulness of Hogs. ("Hand For the Hog").
Huck flees to the nearby Jackson's Island, where he, alone, asserts his self-assurance ("I, Huckleberry, Me"). But Huck isn't alone; Miss Watson's slave, Jim, is there as well. He has run away to avoid being sold down the River to New Orleans. Despite his unease with the concept of abolitionism Huck offers to help Jim reach freedom in the North. A posse is after Jim: with only moments to spare, they find a raft and get it afloat in the of the mighty Mississippi River ("Muddy Water").
Jim and Huck travel only at night and don't get far from Jackson's Island before they are reminded of the seriousness of their actions: a boat carrying runaway slaves back to their masters passes them in the night ("The Crossing"). The days are long as the two forge their way down the river. They pass a flooded house, and a dead man floating in the water that Jim will not let Huck look at. As they sing of the beauty of the River ("River In the Rain") in a fog, they sail past the mouth of the Ohio — their path to freedom. Soon after, they pick up two grifters who commandeer the small raft as they escape the latest mob on their tail. The con men claim to be a Duke and a King, the long lost heirs to the Duchy of Bridgewater and the French Throne. Huck is intrigued by the delinquent "royals". The King and the Duke commandeer the raft and plot to sell Jim back into slavery for their own profit, unbeknownst to Huck ("When the Sun Goes Down In the South").
Huck, Jim, the Duke, and the King wash ashore in Bricktown, Arkansas, and attempt to fleece the rubes they find. The Duke and King come up with a scheme to make money ("The Royal Nonesuch"), tricking the townspeople. By the end of the evening, Huck can appreciate a new way of life — the three are now several hundred dollars richer. When he returns to the raft, Huck plays a horrible trick on Jim by assuming the guise of a slave hunter. Unamused, Jim rebukes Huck for the first time. After some thought, Huck realizes that Jim, though a slave, is still a human being and deserves an apology ("Worlds Apart").
The King and Duke reappear to dragoon Huck into their next escapade. While Jim is, again, left alone with the raft, the three encounter a young fool on a dock, singing of his love of his home state ("Arkansas"). Through no fault of his own, he tells the con men everything they need to know about a fortune to be inherited in the Wilkes family, and they crash the funeral as impostors to go about securing their riches ("How Blest We Are"). Huck — through it all a pure soul — sees that the beautiful and innocent Mary Jane Wilkes is being robbed of her rightful inheritance by these "rapscallions", and steals back her money from the King and the Duke as she mourns her father's coffin ("You Oughta Be Here With Me"). He quickly stuffs the gold into her father's coffin and hides behind it to avoid notice.
When Mary Jane realizes what Huck has done, she asks that he remain with her and become her friend. For the first time in his life, he is moved by the actions of another ("Leavin's Not the Only Way To Go"), yet he realizes that he has made a promise to Jim: one that transcends mere friendship. Huck returns again to the raft and finds the Duke tarred and feathered: he has sold Jim back into slavery for a mere forty dollars. Feeling guilty about what he has done, Huck pens a letter to Miss Watson, telling her where she can find the runaway Jim. After a momentary reprieve, Huck ends up feeling worse than ever. He tears up the letter and resolves to free Jim again, even if it means he will go to Hell ("Waiting For the Light To Shine" (Reprise)).
Huck visits Mr. Phelps, the farmer to whom Jim has been sold, and is shocked to discover that he has been mistaken for Tom Sawyer, the Phelps' nephew who is expected for a visit. Tom arrives later and is intercepted by Huck before he reaches the farm. Huck explains everything and Tom, delighted by the prospect for a grand adventure, decides to help Huck free Jim from his captors while pretending to be his own brother Sid. They find Jim imprisoned in a tiny cell and work to free him as he laments his desire to be free ("Free At Last"). Progress is slowed by Tom's insistence of making sure that the circumstances of the escape match the adventure novels he has read, which includes notifying Phelps of the escape by an anonymous letter. As they free Jim, Tom is shot in the leg. Jim sacrifices his freedom to ensure Tom gets a doctor, and is about to be locked up again when Tom admits that Miss Watson has died, freeing Jim in her will.
Jim decides to continue his trek to the North so that he may buy his family out of slavery, and Huck decides to continue westwards to escape any attempts to "civilize" him. They sit for a moment at the banks of the river, recalling their adventures together ("River In the Rain" (Reprise)). Jim reveals to Huck that the body they saw in the water was the dead body of Huck's Pap. Jim leaves Huck alone for the last time, and Huck decides, "It was like the fortune Jim predicted long ago: considerable trouble and considerable joy." He begins his next journey ("Muddy Water" (Reprise)).