The first time we meet Tom Sawyer, he's in Aunt Polly's pantry, stealing from the jam jar. This is only the beginning of his rascally adventures. Tom narrowly escapes being hit by Polly, then plays hooky for the rest of the day. When Aunt Polly finds out about this – thanks to Tom's snitch of a brother Sid – he's sentenced to whitewash a fence the next day. But Tom gets out of the punishment by tricking the local boys into paying him for the privilege of whitewashing the fence. Tom heads off to enjoy himself.
On his way back home, he sees a girl standing in Jeff Thatcher's house. He falls hopelessly in love and starts showing off for her. The next day, in Sunday school, Tom uses the loot he made with the fence scheme to buy a bunch of "tickets" from the other boys. He uses these tickets to get himself a Bible prize. But Tom makes a fool of himself in front of a visitor, Judge Thatcher, and the rest of the Sunday school crowd, when he tells them all that the first two apostles were named "David and Goliah."
Before school the next day, Tom runs into Huckleberry Finn. Huck is the son of the town drunk and he has no mother, so he basically gets to do whatever he wants. Everyone, including Tom, envies Huck. Tom and Huck start discussing various ways to cure warts, and then agree to meet up at the graveyard at midnight to try out a new cure involving a dead cat.
Tom shows up at school late, prepared to make up an excuse, when he notices that the only seat open on the girl's side is next to that girl. So when the schoolmaster asks him to explain himself, he tells him that he's been talking to Huckleberry Finn, which shocks the schoolmaster. Tom is whipped and then "forced" to go sit next to the girl. Tom impresses her with his awful drawing skills, then introduces himself. The girl's name is Becky. Just before Tom is pulled away by the schoolmaster for being disorderly, they agree to meet outside during recess.
During recess, Tom gets Becky to tell her she loves him and to give him a kiss, but he mucks it all up when he mentions his old flame Amy Lawrence. He tries to make up by giving Becky a gift, but she throws it to the ground. Tom runs off to the woods and sulks for a while, but before too long he's dreaming about being an "Indian" and a pirate. His fantasy is interrupted by Joe Harper, and the two boys play Robin Hood for the rest of the afternoon.
That night, Tom sneaks out of the house and heads over to the graveyard with Huck Finn. Just as they are approaching, three men appear: Dr. Robinson, Injun Joe, and Muff Potter. The boys watch in horror as Injun Joe murders Dr. Robinson during a fight, and blames it on Muff Potter who, already drunk, had been knocked out in the middle of the scuffle. They run away as fast as they can. Once they've settled down, they promise never to tell anyone about what they've seen, write up a contract, and sign it in blood.
The next morning, Tom is scolded by Aunt Polly; he gets whipped for playing hooky when he shows up at school and, to top it all off, he finds his andiron knob left on a desk.
By noon that day, word about the murder has gotten around, and school is let out. Everybody heads over to the graveyard. Soon, Muff Potter shows up, in the company of the Sheriff. Muff Potter swears he's innocent, but Injun Joe has already sold him out. Tom and Huck watch in horror, realizing nothing is going to be done about Injun Joe. Tom is so afraid that he talks in his sleep about the murder, and has to fake a toothache and tie up his mouth to prevent himself from letting anything slip. Though he doesn't dare to say anything about the murder, Tom stops by the jail whenever he can to bring gifts for Muff Potter.
Soon, however, Tom falls into a deep depression. Aunt Polly attempts to help him by administering all sorts of medicines, but none of them work. Tom feeds a bit of one to the family cat, which causes the cat to go crazy. When Aunt Polly yells at him, Tom finally tells her that her "cures" don't work, and she apologizes.
Feeling better about himself, Tom heads to school hoping to see Becky Thatcher. When she tells him to get lost, he falls back into a depression and ditches the schoolhouse. He runs into Joe Harper, who has just been scolded for drinking cream, and the two decide to abandon civilization, head off to Jackson's Island and become pirates. They take Huck Finn along for the ride.
After getting supplies – a.k.a. stealing some bacon, a ham, and other provisions – they set out for the island. Though Tom and Joe at first feel pangs of conscience, soon enough they're off relaxing, enjoying nature, swimming, and fishing. At some point, they notice a ferry, off in the distance, filled with people. They figure out that the people are a search party; someone has drowned. Soon the boys realize that they are the ones who have supposedly drowned. This makes the boys very happy. Joe begins to show signs of homesickness, but Tom manages to make him think twice.
After Huck and Joe have nodded off to sleep, Tom has a brilliant idea. He writes two notes, leaves one by the camp – along with some marbles and toys – and takes the other with him. He swims over to the Illinois shore, then sneaks aboard the ferry back to St. Petersburg. Once there, he goes to his house, and listens in as Aunt Polly, Mrs. Harper, Sid, and Mary talk about him and Joe; he takes great pleasure in hearing them praise him. When Aunt Polly goes to bed, Tom goes up to her and considers leaving his note next to her bed. At the last minute he decides against the plan, kisses her, and leaves.
He gets back to Jackson's Island early that morning, takes a nap by the shore, and then heads over to the camp. He surprises Huck and Joe, who are puzzling over his note – which says they can have his stuff if he isn't back by breakfast.
The next day, after more of the same kind of fun, Joe and Huck begin to get homesick. Tom convinces them to stay by telling them "his secret." That night, there's a terrible thunderstorm, which they manage to survive, and they spend the next day pretending to be Indians.
The next day, the townspeople have assembled in church for the boys' funeral. Just after the preacher gives his sermon praising the saintly departed children, Tom, Huck, and Joe come out of nowhere and march down the aisle. Turns out they came back to town the night before and waited in the church until this moment to show their faces. Later on, Tom tricks Aunt Polly into thinking he's psychic by telling her all about the conversation he eavesdropped on when he snuck home from Jackson's Island.
The boys are treated as heroes at school. Tom, still mad at Becky, ignores her and flirts with Amy Lawrence instead. In order to get back at Tom, Becky invites everyone within earshot to a picnic – except Tom and Amy – but when this doesn't work she's forced to try another plan. When Tom sees her reading a book with another classmate, he gets angry and leaves.
Aunt Polly finds out that Tom's whole "psychic" bit was a scam, and she confronts Tom. She's angry that he didn't let her know he was still alive. He tells her that he thought about doing so – which he did – but she has a hard time believing him until she finds the note in his pocket.
The next day at school, Tom sees Becky peeking at the schoolmaster's special anatomy book. When she sees Tom, she tries to put the book away as quickly as possible, but rips a page in the process. When the schoolmaster finds the torn page and starts asking who ripped it, Tom lies and takes responsibility so that Becky doesn't have to get punished. He's whipped, but he doesn't mind.
Summer vacation rolls around and Tom finds himself incredibly bored. The murder trial starts, however, and he and Huck both become consumed with guilt. Finally, Tom breaks down and testifies on the last day of Muff Potter's trial, saving Muff. Injun Joe flees the courtroom before anyone can react.
Tom is hit by treasure-hunting fever, and he enlists Huck to help him look. The two boys decide to search inside a "haunted" house one night. Their hunt is interrupted by the appearance of two men, one of whom turns out to be Injun Joe dressed as a "Spaniard." Tom and Huck watch as Injun Joe happens upon a box of gold coins buried in the floor. Injun Joe, who has been using the place as a safehouse, becomes suspicious when he sees the boys' tools in the corner, and takes the coins with him. The boys only narrowly escape being found.
Tom and Huck hear Injun Joe mention a hiding place, "Number Two, under the cross," which they determine to be in a room at one of the town's taverns. Tom sneaks into the room one night and finds Injun Joe drunk on the floor. Huck agrees to stand watch outside the room every night, until he sees some activity.
Becky's picnic rolls around and Tom forgets about the treasure. Tom and Becky head into the local cave along with the rest of the kids. That night while on lookout duty, Huck sees two shadowy figures enter the room, then exit with a box. He follows them to just outside the Widow Douglas's house, where he hears the men, who turn out to be Injun Joe and his partner, discussing their "revenge." Huck gets the help of the Welshman, a man who lives nearby, then runs away as fast as he can. The next morning, he returns to visit the Welshman, who tells him that the two men got away. Huck reveals that one of the men was Injun Joe and promptly falls sick.
Meanwhile, Tom and Becky are lost in the cave. They attempt to find their way out to no avail and, because Tom and Becky lied and said they were going to spend the night at the Harpers' house, no one notices until Sunday morning. Rescuers, including Judge Thatcher, are dispatched.
Tom continues to look for a way out of the cave, and thinks he's found one when he sees a rescuer coming around the corner in the cave, but it's Injun Joe. Luckily, Tom escapes unnoticed. Eventually, he is able to find his way out of a small hole and heads back in to town with Becky. Once Tom is fully recuperated, he goes to visit Becky. He runs into Judge Thatcher, who tells him that the entrance to the cave has been sealed with a metal door. Tom tells the judge that Injun Joe was in there. The townspeople rush out to the cave and find Joe dead by the door.
Soon after, Tom goes and tells Huck that he knows where the treasure is. He takes him to the cave, where they find Joe's hideout, and, hidden in a secret chamber, under a cross, the treasure. They are intercepted on their way back home by the Welshman, who takes them to the Widow Douglas's house. Once there, Huck's bravery is revealed, and the Widow tells everyone that she will be taking care of the boy from now on.
Tom runs and gets the money, then dumps it on the table. It is split into two shares, and both Tom and Huck receive a considerable income as a result. Huck soon tires of living with the Widow, but Tom convinces him to go back and live with her.