Tom Sawyer [Josh Albee] and Huckleberry Finn [Jeff Tyler], hungry for adventure and lured by superstition, skip school to perform an incantation they believe will resurrect a dead cat, hoping the ritual will be empowered by the imminent death of a man named Hoss Williams. During their audacious stunt, they cross paths with Muff Potter [Buddy Ebsen], the town drunk, and Injun Joe [Vic Morrow] interrupts to tell them that Doc Robinson wants their help to exhume Williams’ body. Concurrently, Tom dodges meals and school by weaving elaborate stories about his whereabouts at dinner, while Aunt Polly [Jane Wyatt]—his guardian—tries to discipline him for truancy, only for Tom to cunningly enlist other children to take on his chores.
Following Williams’ death, Tom and Huck go to the cemetery and stumble upon Muff Potter and Injun Joe digging up the grave under the orders of Doc Robinson. An argument over additional payment erupts, and Joe drives a shovel into Muff, while Joe knocks Robinson into the grave and fatally stabs him with Muff’s knife. Horrified, Tom and Huck witness the whole scene and flee, binding themselves with a pact of silence about the murder they observed. In the aftermath, Injun Joe deceitfully accuses Muff Potter of the crime, and Muff is quite suddenly imprisoned.
Meanwhile, Tom’s attention is drawn to the newly arrived Becky Thatcher [Karen Pearson], and their budding connection adds a hopeful thread to the grim events unfurling in town. At Muff Potter’s trial, as Injun Joe testifies with false claims, Tom—unable to bear the injustice—musters the courage to tell the true chain of events on the stand, carefully omitting Huck’s presence. In a dramatic turn, Injun Joe hurls a knife at Tom, narrowly missing him, and then makes a daring escape through the courthouse window.
Tom’s romance with Becky Thatcher deepens, even as trouble looms over his earlier actions; Becky learns of Tom’s prior commitment to Amy Lawrence, which complicates their relationship. The pair decide to run away together, setting off on a riverbound adventure down the Mississippi. Their raft is capsized by a riverboat, stranding them on a remote island, where they witness a river-dragging operation—cannons fired to recover bodies from the water.
Yearning for home, Tom and Huck return and discover their own funeral in progress, interrupting the service with their dramatic reappearance. The town’s order is upended as Huck receives care from the Widow Douglas and a sense of belonging begins to take root, while Tom embraces a path toward growth and reconciliation with his family.
Back in town, the two boys plan another escape, but the day’s chaos continues to unfold. During Independence Day festivities, Tom and Becky explore McDougal’s Cave, leading to a perilous chase that brings them face-to-face with Injun Joe. A tense confrontation culminates in a blaze of danger, with Muff Potter’s torch accidentally setting the stage for Joe’s fall to his death. The resolution features a mix of fear, relief, and the realization that their choices have real consequences.
In the aftermath, Huck vanishes for a time, prompting concern from the Widow Douglas as Tom tracks him down at their favorite fishing spot, chiding him for his thoughtlessness. Tom also learns that Muff Potter intends to leave town, and Judge Thatcher arranges a two-week trip to St. Louis for Tom and Becky, offering a chance for new experiences and healing. In the end, Tom mends fences with his family and commits to personal growth, while the town slowly comes to terms with the secrets, loyalties, and courage that shaped their storms and songs.