This story takes place about two decades before the Civil War in St. Petersburg, a small Missouri village on the Mississippi River. The main character is Tom Sawyer. Tom's mother is dead and he lives with his Aunt Polly. Other members in the house consist of Tom's cousin Mary and his brother Sidney.
One day Tom decides to go swimming instead of going to school, so his Aunt Polly forced him to spend a Saturday white washing the fence. That same day after playing with his friend Joe Harper, Tom is walking and home and falls in love with the new girl, Becky Thatcher.
Being told not to mess with Huckleberry Finn, an abandoned son of a drunk, Tom goes to the cemetery anyway with Huck. In the cemetery that night, Tom and Huck come across Dr. Robinson, a young doctor, Injun Joe, a sinister half breed, and Muff Potter, a weak man fond of drinkers, digging up a recently buried corpse.
A conflict occurred between Injun Joe and Dr. Robinson and Injun Joe stabs the doctor to death and knocks Muff Potter unconscious. Not knowing who to blame, Muff blames this on himself which he tells the court.
Tom, Huck, and Joe decide to become pirates and establish themselves on Jackson's Island. Being gone for three days, the town's people declare that Tom and Joe are officially dead. Not knowing that they were declared dead, Tom sneaks back into his house and hides under a bed. Tom over hears a conversation between his Aunt Poll, Mary, Sidney, and Joe Harper's mom. Aunt Polly and Mrs. Harper were crying and saying that their kids were unselfish. Tom also over hears that the boy's funerals will be preached the following Sunday morning. After Aunt Polly has gone to sleep Tom kisses his aunt and heads back to the island to tell the others. The three plot a scheme and walk in during the sermon. The children and family embrace for they are reunited.
In the courthouse for the sentencing of Muff Potter, Tom explains that Muff Potter is not guilty of murder. Injun makes his escape through a window in the court room.
The boys decide to hunt for treasure in an abandoned house and see Injun Joe once again taking the treasure he had found. Tom and Huck decide to follow Injun Joe. Huck is named the overnight watchman, while Tom rests until Huck gives a signal of Injun Joe. Tom and Becky decide to go to McDougal's cave and accidentally lost.
The town's people once again begin to worry because the children had been gone for over three days. Tom catches sight of Injun Joe burying treasure under a cross and quickly flees away. Tom finds an opening and he and Becky go home.
Two weeks later the mouth of McDougal's cave is sealed. When Tom hears this, he tells Judge Thatcher that Injun Joe is still in the cave. The judge opens the cave to find Injun Joe dead on the cave floor. Tom and Huck go back to the cave and recover the treasure under the cross. The total amount of money in the box was $12,000. Huck is taken to the home of Widow Douglas, a kind woman in town and lives with her.