The Adventures of Tom Sawyer revolves around the youthful adventures of the novel's schoolboy protagonist, Tom Sawyer, whose reputation precedes him for causing mischief and strife. Tom lives with his Aunt Polly, half-brother Sid, and cousin Mary in the quaint town of St. Petersburg, just off the shore of the Mississippi River. St. Petersburg is described as a typical small-town atmosphere where the Christian faith is predominant, the social network is close-knit, and familiarity resides.
Unlike his brother Sid, Tom receives "lickings" from his Aunt Polly; ever the mischief-maker, would rather play hooky than attend school and often sneaks out his bedroom window at night to adventure with his friend, Huckleberry Finn the town's social outcast. Tom, despite his dread of schooling, is extremely clever and would normally get away with his pranks if Sid were not such a "tattle-tale."
As punishment for skipping school to go swimming, Aunt Polly assigns Tom the chore of whitewashing the fence surrounding the house. In a brilliant scheme, Tom is able to con the neighborhood boys into completing the chore for him, managing to convince them of the joys of whitewashing. At school, Tom is equally as flamboyant, and attracts attention by chasing other boys, yelling, and running around. With his usual antics, Tom attempts to catch the eye of one girl in particular: Becky Thatcher, the Judge's daughter. When he first sees her, Tom immediately falls in love with Becky. After winning her over, Tom suggests that they "get engaged." But when Tom accidentally blurts that he has been engaged before to Amy Lawrence, he ruins his relationship with Becky and becomes heartbroken.
One night, Huck and Tom sneak off at midnight to the town's graveyard, where they are planning to carry out a special ritual used to cure warts. Believers in superstition and folklore, the two expect the graveyard to be full of ghosts. After hearing voices approach them, the two boys hide in fear; the voices belong to Injun Joe the villainous savage, Muff Potter- the town drunk, and Dr. Robinson. The three men are grave robbing! Soon, a fight breaks out between Dr. Robinson and the two other men. As Dr. Robinson grabs a headboard and knocks the liquored Muff Potter into unconsciousness, Injun Joe grabs Muff's knife and stabs the doctor to death. The boys run away from the graveyard before they learn that Injun Joe is planning on framing Muff for the doctor's murder. Fearful of Injun Joe and horrified at what they have witnessed, Huck and Tom vow to keep silent regarding the night's events.
The next day brings only grief for Tom. Aunt Polly learns from Sid that Tom snuck out the night before and cries over him. At school, Becky snubs Tom by paying no heed to his boyish antics. Hurt and angry, Tom assembles a "gang" of pirates: himself, Joe Harper, and Huck. The three boys decide that they have had enough of normal society and run away to Jackson Island, in the middle of the Mississippi River. When the boys are missing, the whole town assumes that they have drowned in the river and villagers drag the river for their bodies. In the darkness of the night, Tom sneaks off the island to return home and leave a note for Aunt Polly informing her that he is not dead. Instead, he overhears Polly and Mrs. Harper making plans for their funerals. The boys then wait until the morning of their own funeral, sneak back into town and attend their own funerals before revealing to the congregation that they are alive!
At school, the boys are the envy of each pupil; however, Tom has still not won back Becky's heart. When Tom inadvertently catches Becky reading the schoolmaster's book, she jump out of surprise and breaks it. Later that day, when the schoolmaster questions Becky whether it was she who broke the book, Tom lies and says that it was he who committed the act. Although he takes the punishment for Becky, he wins back her love and attention.
After school is let out for the summer, Muff Potter's trial begins. The town of St. Petersburg has already convicted the innocent man in their minds. Tom and Huck are both racked by their guilty consciences, and are made to feel even worse when Muff Potter thanks them for being kind to him. When the trial begins, the defense council calls Tom Sawyer to the witness stand. To the surprise of Huck, Muff Potter, and all those who are in the audience, Tom divulges all he knows about the murder, naming Injun Joe as Dr. Robinson's killer. Before the trial ends, Injun Joe sprints out of the courtroom before anybody can catch him.
Injun Joe is declared missing and Muff Potter is set free with the apologies of the town. Meanwhile, Tom is afraid that Injun Joe will attempt to seek revenge on him for being a witness, and Huck holds similar fears. One day, Huck and Tom decide to dig for buried treasure at the old haunted house on Cardiff Hill. As they begin their search, the entrance of two strange men surprises the boys. In hiding, Tom and Huck realize that one of the men is Injun Joe in disguise as a deaf-and-dumb Spaniard. Tom and Huck watch as Injun Joe and his accomplice discuss plans for a "revenge job." The two villains are planning to hide a bag of six-hundred dollars in the haunted house and meet back there; but when they hide their bag of money, they discover a box of buried treasure that has already been hidden in the haunted house treasure that once belonged to a gang of robbers. The villains decide to hide their loot in "Number Two" under "the cross" and exit the house. Obsessed with obtaining the treasure, Tom and Huck make plans to follow Injun Joe and find out where the treasure is buried.
Becky, who has been out-of-town, returns to St. Petersburg and holds a picnic for all of her friends. As part of the picnic festivities, the children go exploring in MacDougal's cave: a large cave with secret underground passageways. Unbeknownst to the other picnickers and adults, Tom and Becky lose themselves within the depths of the cave.
In the meantime, Huck has resigned himself to waiting outside the Temperance Tavern, where they suspect Injun Joe is staying. On the brink of giving up, Huck's patience is rewarded when the two villain step out into the night and head off towards the haunted house. But instead of entering the haunted house, the villains go toward the old Widow Douglas's house, with the intention of torturing and maybe even killing her. Remembering times when the widow bestowed her kindness upon him, Huck races toward the Mr. Jones's house, informing him of Injun Joe's plans to hurt the widow. Mr. Jones and his two younger sons hurry over to the widow's estate and scare off Injun Joe and his accomplice before any harm is done.
The word of Widow Douglas's near attack is circulated around town. But news of the missing children breaks out, and for the moment, the entire town concentrates on praying and searching for Tom and Becky. Deep within the cave, Tom and Becky have lost all sense of direction. With the last of their candle burnt out and no food to eat, the two are aware that they may starve to death. Tom attempts to comfort Becky, and continues to explore the cave's passages in hoping of finding a way out. Winding down one passageway, Tom sees a man and shouts to him; to his surprise, the figure belongs to Injun Joe! Frightened by Tom's shouts (and not recognizing the boy's voice), Injun Joe runs away. Tom never tells Becky of this incident, for fear that we would cause her even more worries. Eventually, Tom's persistence pays off when he discovers a tiny hole that the children manage to crawl through and escape peril.
With the safe return of Becky and Tom, the town of St. Petersburg rejoices. Judge Thatcher orders that the door to MacDougal's cave be locked and sealed with metal. When Tom learns of this, he tells finally tells the Judge that Injun Joe is in the cave. Upon breaking the sealed door, Tom, the Judge, and the other citizens find Injun Joe at the mouth of the cave, starved to death.
When he meets up with Huck, Tom informs him that he knows where the treasure is buried. Mistaking the treasure for lost, Huck is eager to return to MacDougal's cave with Tom in search of the money. After recovering the treasure from the cave, the two boys return to town, only to be ushered into the Widow Douglas's parlor. To express her gratitude towards Huck for saving her life, the widow intends on giving Huck a permanent home and providing him with an education. Declaring that Huck is now independently wealthy, Tom spring forward with their newfound treasure, totaling over twelve thousand dollars.
The novel ends with Huck and Tom discussing their future plans of becoming world-class robbers.