That Sunday, the whole family must go to church. At Sunday school, Tom trades other boys for tickets that will earn him a free Bible. To actually earn the Bible, children must collect tickets by learning two thousand Bible verses. Tom's new love, Becky Thatcher, arrives at Sunday school with her father, a judge. Tom proudly claims his Bible in front of everyone, but cannot name the first two disciples when questioned by Judge Thatcher. At church, he entertains himself by playing with a pinch bug, which bites a dog and causes a huge disruption.
On his way to school on Monday, Tom runs into Huckleberry Finn, the son of the town drunk. Huck is homeless, can't read and lives a wild life. Tom is late for school, and for punishment is forced to sit next to Becky, which he is happy about. At lunch, Tom and Becky meet and Tom convinces her that they should get engaged and kiss. She does kiss him, but Tom lets it slip that he was already engaged to someone else, and she rejects him. Tom skips the rest of school and meets Joe in the woods to play Robin Hood.
At midnight, Tom and Huck sneak into the graveyard. Once there, they hear people coming and hide. Dr. Robinson arrives with Injun Joe, an evil criminal, and Muff Potter. They are stealing bodies from the grave. The men argue. Muff Potter is knocked out, and Injun Joe murders Dr. Robinson. Tom and Huck run away, fearing for their lives. When Muff Potter awakes, Injun Joe tells him that he, not Injun Joe, murdered the Doctor.
Tom and Huck, scared, swear never to tell anyone what they saw. However, Tom is bothered by the event and begins to have nightmares. Becky gets sick and he becomes very depressed. When Becky returns to school, she rejects him again and Tom decides to run away.
He convinces Joe and Huck that they should become pirates, and they steal a skiff and sail to Jackson's Island, down-river from St. Petersburg. There they play and talk about what they will do as pirates. They see people from the village searching the river for them, and realize that they townsfolk believe that they have drowned. They begin to get homesick, but Tom convinces them that they should stay on the island. That night, however, he sneaks back to St. Petersburg.
Tom intends on leaving Aunt Polly a note saying that they are alive and well. When he sneaks into his house, he hides and listens to Aunt Polly, Joe's mother, his brother Sid, and his cousin Mary crying and talking about funeral plans for the boys. Tom waits until Aunt Polly is asleep and sneaks back out, without leaving the note.
After Tom returns to the island, he tells Huck and Joe of a great plan he has devised. Huck teaches them how to smoke, although they get sick doing it. That night, there is a terrible storm, and the boys spend most of the night getting soaked and trying to find shelter. The day of the funeral, they act on Tom's plan: they return to the village and hide in the gallery of the church to watch their own funeral. In the middle of the funeral, they come out of hiding and the entire town is overjoyed.
Back at school, Tom and Becky are still fighting. Becky accidentally rips a page in the schoolmaster's book, but Tom, out of love, pretends he did it and takes the punishment for her. She is grateful and their fighting stops.
School ends with the boys playing a prank on the schoolmaster in front of the whole village. Becky leaves town for the summer, and Tom is sad and very bored. Tom gets the measles and is sick for two weeks. A revival comes to town and everyone, even Huck, gets very religious for a short time.
Soon enough, that ends, just in time for Muff Potter's trial to begin. Tom is still wracked with guilt about letting Muff Potter take the blame for Injun Joe's crime. He goes against his oath and confesses what he knows to the defense attorney. He testifies in court, and Muff Potter is freed, but not before Injun Joe escapes.
Tom and Huck go looking for buried treasure. Instead, they find Injun Joe again. While hiding from him, they discover that he is in possession of a large amount of treasure. They decide to spy on him and try to steal it. Becky returns to town, and all the children (except Huck) go on a picnic to McDougal's Cave. While exploring, Tom and Becky get lost and left behind.
The same night Tom and Becky get lost, Huck follows Injun Joe and another man to Widow Douglas's house. He overhears Injun Joe's plan to hurt the Widow Douglas, and runs to Mr. Jones, the Welshman, to get help. Mr. Jones and his sons chase Injun Joe off. The next day, Huck is exhausted and gets very sick. At church that morning, Aunt Polly realizes that Tom and Becky are missing, and the town begins to search the maze-like cave to find them.
Inside the cave, Tom and Becky realize they are lost and try to find a way out. At one point, Tom thinks he's found someone, but all he discovers is Injun Joe hiding out in the cave. After many days, just as they've given up hope, Tom sees light and leads Becky out. The townsfolk are overjoyed when they return. Judge Thatcher has the door to the cave sealed. When Tom finds out, he tells the judge that Injun Joe is inside, but they arrive too late, and Injun Joe has starved to death.
After Injun Joe's funeral, Tom realizes that the treasure is hidden in the cave. He and Huck go back and find the treasure. When they return, they are summoned to the Widow Douglas's house, where Mr. Jones tells everyone that Huck is the one who saved the Widow's life. The Widow, out of gratitude, announces that she will adopt Huck. Tom reveals that they have found Injun Joe's treasure. They are both rich.
Huck has a hard time living under Widow Douglas's roof and runs away. Tom convinces him to return and become a part of respectable society with the promise that they will start a dangerous gang of robbers. Huck agrees, and they go back to the village.