Tom Sawyer lives with his Aunt Polly and his half-brother Sid. He skips school to swim and is made to whitewash the fence the next day as punishment. He cleverly persuades his friends to trade him small treasures for the privilege of doing his work.
Tom falls in love with Becky Thatcher, a new girl in town, and persuades her to get "engaged" by kissing him. But their romance collapses when she learns Tom has been "engaged" previously to Amy Lawrence. Becky cried for a great deal of time until the other students began to notice, and she became embarrassed. Shortly after Becky shuns him, he accompanies Huckleberry Finn to the graveyard at night, where they witness a trio of body snatchers, Dr. Robinson, Muff Potter, and Injun Joe, getting into a fight in which Robinson is murdered by Injun Joe. Tom and Huckleberry Finn swear a blood oath to not tell anyone about the murder, as they feel that if they do, Injun Joe would murder them.
Bored by school, Tom, his best friend Joe Harper, and Huck run away to an island in the Mississippi called Jackson's Island. While enjoying their new-found freedom, they become aware that the community is sounding the river for their bodies. Tom sneaks back home one night to observe the commotion. After a brief moment of remorse at his loved ones' suffering, he is struck by the idea of appearing at his own funeral. The trio later carry out this scheme by making a sensational sudden appearance in the church in the middle of their joint funeral service.
Back in school, Tom gets himself back in Becky's favor after he nobly accepts the blame and punishment for a book she has ripped.
In court, Joe pins the murder on Muff Potter, but Tom and Huckleberry Finn know he is innocent. At Potter's trial, Tom decides to speak out and Joe escapes through a window before he can be apprehended. Henceforth the boys live in constant fear of Joe's revenge on them for incriminating him.
Summer arrives, and Tom and Huck go hunting for buried treasure in a haunted house. After venturing upstairs they hear a noise below. Peering through holes in the floor, they see Injun Joe disguised as a deaf-mute Spaniard; Injun Joe and his companion plan to bury some stolen treasure of their own. From their hiding spot, Tom and Huck wriggle with delight at the prospect of digging it up. By chance the villains discover an even greater gold hoard buried in the hearth and carry it all off to a better secret hiding place. The boys are determined to find where it has gone. One night Huck spots them and follows them. He overhears their plans to attack the wealthy Widow Douglas. By running to fetch help, Huck prevents the crime and becomes an anonymous hero.
In the meantime, Tom goes on a picnic to McDougal's Cave with Becky and their classmates. Tom and Becky get separated from the others and wander lost in the extensive cave complex for the next few days. Becky gets extremely dehydrated and starved, so Tom's search for a way out gets even more desperate. He accidentally encounters Injun Joe in the caves one day, but is not seen by his nemesis. Eventually, he finds a way out, and they are joyfully welcomed back by their community. As a preventive measure, Judge Thatcher, Becky's father, has McDougal's Cave sealed off with an iron door, but this traps Injun Joe inside. When Tom hears of the sealing several days later and directs a posse to the cave, they find Injun Joe's corpse just inside the sealed entrance, starved to death.
A week later, having deduced from Injun Joe's presence at McDougal's Cave that the villain must have hidden the stolen gold inside, Tom takes Huck to the cave and they find the box of gold, the proceeds of which are invested for them. The Widow Douglas adopts Huck, but he finds the restrictions of a civilized home life painful. He attempts to escape back to his vagrant life. Tom tricks him into thinking that he can later join Tom's new scheme of starting a robber band if he returns to the widow. Reluctantly, Huck agrees and goes back to her.
See also List of Tom Sawyer characters.