When the curtain rises, we see Tom Sawyer fishing happily in a meadow outside of St. Petersburg, Missouri, in 1840. When his friends arrive, he joins them in a game of Robin Hood. Tom's strict, but kindly, Aunt Polly sends him off to school, where he tricks the schoolmaster, Mr. Dobbins, into letting the class have the day off.

The next morning, Aunt Polly orders Tom to whitewash the fence in front of their house. Tom's half-brother, Sid, an insufferable goody-goody, couldn't be happier. Frustrated, Tom sings about his plan to run away someday and have adventures ("Here's My Plan").

As Tom procrastinates, he meets a beautiful newcomer to the town, Becky Thatcher. They're instantly attracted to each other. Next, along comes Tom's best friend in the world, the town's outcast, Huckleberry Finn. When Huck comments that painting the fence looks like fun, Tom gets an idea. Moments later, Tom tricks his schoolmates into painting the fence for him... and paying for the privilege ("Smart Like That")!

That night, Tom and Huck go on an adventure and visit the local graveyard. There, hidden behind a gravestone, they see the troublemaking Ol’ Man Joe and have a fight with Doc Robinson, the local doctor ("Hands All Clean"). Before long, Joe murders Doc Robinson before their very eyes! The boys run off and swear in blood to keep mum forever about the bloody deed ("The Vow"). Meanwhile, Ol’ Man Joe arranges to have a local vagrant, Muff Potter, blamed for the murder.

On the way to school the next day, Tom tries to convince Huck to learn to read, but Huck is afraid. A few minutes later, Huck saves kindly old Widow Douglas from the advances of the town drunk. In gratitude, she offers to teach Huck how to read; in fact, she offers him her home as a place to live. Huck promises that he will think about it.

In school that day, Tom saves Becky from getting into trouble. Moments later, they declare their undying love for each other ("To Hear You Say My Name").

A few days later, Muff Potter is arrested for murder. Muff doesn't realize that Ol’ Man Joe has framed him and he pleads with Joe to save him from hanging. Joe says that he'll help, provided that Muff gives him a map that Muff has found – a map leading to that legendary treasure, Murrell's Gold.

As Muff is taken to jail, Tom faces a terrible choice: Should he tell the truth about the murder and save Muff Potter, thereby incurring the wrath of Ol’ Man Joe? Or should he keep his vow to Huck and let Muff hang?

At Muff Potter's trial, Tom takes the stand. He tells the truth and swears that Ol’ Man Joe committed the murder. Ol’ Man Joe springs from his seat and screams "You are dead, boy!" He throws a knife at Tom, then races from the courtroom amid a hale of gunfire.

A few weeks later, Huck comes to warn Tom that Ol’ Man Joe has returned to town and that he needs to be "prepared" for him, for he is the one that Joe wants to kill.

The next morning, after weeks of secret tutoring bythe  Widow Douglas, Huck at last learns how to read. He and the Widow celebrate with a song of joy ("I Can Read!").

This is the day of the annual town picnic, and the festivities begin with the exploration of McDougal's Cave, a cavern of frightening size and darkness.

Now, however, a tragedy occurs. Tom and Becky get lost in the cave. Aunt Polly and Judge Thatcher are frantic, and they  begin searching for the two children, as the rest of the town helps.

Underground, Tom and Becky desperately try to find a way out of the cave. Tom assures Becky that they'll succeed ("Light"). When Becky is alone for a moment, Ol’ Man Joe springs from a passage and grabs her, demanding to know where Tom is. Suddenly, Tom jumps out from behind a rock, and a moment later, Huck shows up. With great courage, the three friends battle Ol’ Man Joe and defeat him.

Although badly shaken, the children find Murrell's Gold, a vast treasure of gold coins. Moments later, they see a ray of daylight shining through a crack in the wall. Exhausted, they crawl out of the cave, safe at last.

That same day, the people of St. Petersburg are holding a funeral service for the lost children. During the service, Tom, Huck and Becky limp into town. They peek into the church... and realize that they're watching their own funeral!

When the children are discovered, the town goes wild with happiness. Aunt Polly is overjoyed to have Tom back. Sid is not.

In the final moments of the play, Huck reveals to Tom that he's learned how to read, and the two friends run off to celebrate with the rest of the town ("Finale").