Aunt Polly searches and screams for Tom Sawyer: she wants to confront her nephew about some missing jam. Tom, however, is able to outwit his aunt and slips away. But Aunt Polly loves him so much she cannot be too harsh with him. She is concerned that he will play hooky that afternoon, and sure enough he does.
During the afternoon, Tom meets a boy from St. Louis with whom he fights. That night at home, Tom's clothes are so soiled from the fight that Aunt Polly punishes him by taking away his Saturday's freedom and assigns him the unpleasant task of whitewashing the fence.
On Saturday morning, the forlorn Tom begins his tedious task of whitewashing the fence, fully aware that all of his friends are playing in the town's square. As he begins his task, Aunt Polly's slave, Jim, comes by and Tom tries to bribe him into helping, but Aunt Polly sends Jim on his business. Suddenly, Tom is horrified because one of his friends is about to come by and see him actually working on a Saturday morning. Tom pretends that what he is doing is not work because he is so thoroughly enjoying himself. Soon Ben wants to try his hand and offers Tom his apple. As Ben is painting, other friends come by and also want to try their hands at this fun game. Each boy gives Tom some sort of prize for allowing him to do some whitewashing, and Tom ends up with his fence whitewashed and a small treasury of gifts.
After the fence is painted, Tom heads for the square and, on the way, stops to watch a very pretty young girl who is moving into a house down the street. He shows off for her, and she pretends to ignore him. He is attracted to her and finds out her name is Becky Thatcher. He joins his friends in fun and games where he is the leader of an army which defeats the opposing army. The next day, Sunday, he is forced to attend Sunday school and is bored with the tedium but finds ways to distract himself.
Monday, after offering many excuses for not going to school, he is finally forced to go. On the way, he meets Huckleberry Finn, the son of the town drunk. Huck never goes to school and is the envy of all the boys because of his complete freedom. Huck arranges for Tom to meet him that night so they can bury a dead cat in the cemetery. At school, Tom is punished for being late and is required to sit in the "girls' section." This pleases him because the only empty seat is next to Becky Thatcher. At lunch, he meets her, and they pledge their troth to each other.
At midnight, Huck arrives, and they go to the cemetery where they come upon Dr. Robinson, Injun Joe, and Muff Potter who are digging up a recently buried corpse. There is an argument, Muff is knocked unconscious, and Injun Joe murders the doctor and places the murder weapon next to Muff. The horrified boys flee and take a blood oath never to reveal what they have seen. The next day, the town is in an uproar (school is dismissed), and Injun Joe identifies Muff Potter as the murderer. Tom is fearful that Injun Joe will discover that he was a witness.
Tom, his friend Joe Harper, and Huck Finn decide to become pirates. The three boys find a raft and establish camp on Jackson's Island, where they enjoy a carefree life of fishing, swimming, smoking, and exploring and playing. When a steamboat filled with most of the important townspeople passes by firing cannons over the water, the boys realize that they are presumed to be drowned. Tom sneaks home at night in order to leave Aunt Polly a reassuring note that they are all right, but he changes his mind when he overhears that church services are planned for the "deceased boys" if they are not found by Sunday. The funeral services are secretly attended by the boys, and all rejoice when the dead boys casually stroll down the aisle.
Back at school, Tom finally wins Becky's heart when he takes the blame for one of her indiscretions and heroically suffers the punishment for her misdeeds.
At Muff Potter's trial, it is generally accepted that Muff Potter killed Dr. Robinson and will be hanged. Tom, in spite of his oath with Huck to not reveal what he has seen, cannot stand to see an innocent person hanged for a crime he did not commit. He bravely relates what actually happened. Injun Joe makes his escape by jumping out the second story window.
One day, while Tom and Huck are looking for buried treasure, they explore an old abandoned house. When two men arrive, the boys are trapped upstairs. One man is Injun Joe in disguise. The two criminals retrieve a box of silver coins they had concealed and then, by chance, discover a horde of gold coins that had been buried by some outlaws long ago. They decide to take the gold coins to Injun Joe's other hideout. The terrified boys overhear Injun Joe planning a horrible revenge before leaving the country. The boys fear that they are the subject of his planned vengeance but are fortunate enough to narrowly escape detection. The boys try to discover a place in town that would be the other hideout, but they only find a room filled with an abundant supply of whiskey in a Temperance Tavern.
At the picnic celebrating Becky Thatcher's birthday, several of the boys and girls enter McDougal's Cave. Tom and Becky wander away from the others in search of privacy and become hopelessly lost.
Meanwhile, Huck Finn, who is watching to discover Injun Joe's hideout, follows the two men toward Cardiff Hill, the home of the Widow Douglas and of a Welshman named Jones. Hiding behind a bush, he overhears Injun Joe telling of his intentions to mutilate the Widow Douglas because her husband, the judge, had once had him publicly horsewhipped. Huck hastens to inform Mr. Jones of the plot, and the Welshman and his sons drive off the vicious Injun Joe and his cohort. Huck has been so frightened that he becomes seriously ill, and the Widow Douglas comes to the Welshman's home and nurses the homeless boy back to health.
At the same time, it is discovered that Tom and Becky are missing; they have not been seen since the cave. All the available men in the community meet and carry out a thorough search of the cave. Tom and Becky hear the search party in the distance but are too weak to call loudly enough to be heard. At one point in their ordeal, Tom catches sight of Injun Joe in a nearby passage. After they have been underground for about three days, Tom discovers a way out of the cave. He and Becky then make their way back to the town.
Both are sick for a while, but Tom recovers more quickly than does Becky. Tom also discovers that Judge Thatcher has had the second exit to the cave completely sealed off. Tom reveals that Injun Joe was in the cave. In spite of Injun Joe's evil, Tom cannot let any human face the ordeal of starving that he and Becky just endured. The men go back to the cave and discover Injun Joe's body just inside the cave where he had futilely tried to dig his way out with a knife.
Later, Tom and Huck return to the cave and search for Injun Joe's treasure. After many false starts and using various clues, they recover approximately $12,000 worth of gold coins. This money is invested for them, and they are rich. The Widow Douglas takes Huck into her home to educate him and train him in the ways of civilization. Huck finds schooling, not cussing, and all other things connected with civilization to be completely intolerable, and he runs away. He eventually agrees to give civilized living another try if he can join Tom's band of robbers.