In chapter forty-one Huck finds a doctor to help Tom, but he must lie about how Tom was shot, so he tells the doctor that he kicked a gun in his sleep. Huck then creeps into a lumber pile and accidentally sleeps until morning, so he runs back and comes across Uncle Silas who was wondering where he'd been. Huck lies again and says that he and Sid (meaning Tom) were hunting for the runaway slave. Uncle Silas forces Huck to come home with him, so Huck is unable to find out how Tom is doing, and the family keeps getting more and more worried since he hasn't come home.

Chapter forty-two begins with the doctor and Jim carrying Tom Sawyer back to Phelps farm on a mattress. The doctor informs the family to go easy on Jim since he was very helpful in caring for Tom and willing to risk his freedom to do it, but they locked him back up anyway. When Tom wakes up the next day, he begins talking to Huck about how great it was to set Jim free. Finally, when he finds out that Jim didn't actually escape, he becomes very angry. He informs everyone that Miss Watson died two months ago, and in her will she set Jim free. Then in walks Tom's Aunt Polly who explains to Aunt Sally who Tom and Huck really are and how she tried to write her, but Aunt Sally never got the letters, which Tom admits to stealing except for the last one, which she has but hadn't had time to read.

In the last chapter, they free Jim, and Tom gives him forty dollars for being such a good prisoner. Then they talk about taking him back up on a steamboat and having great adventures. Huck is worried that his dad has probably gotten a hold of all of his money in the time he's been away, but Tom tells him the whole six thousand dollars is still there waiting for him. Then Jim admits that the dead man that they found on the houseboat a while back was Huck's Pap, so he won't cause Huck any trouble any more. Tom decides to wear the bullet they removed from his foot around his neck as a symbol of pride. Aunt Sally offers to let Huck stay on with her, but Huck isn't ready to become civilized again just yet.

These chapters show that despite the uncertainty that living on his own can bring, Huck doesn't really want to be taken in and forced to follow the rules. He enjoys being out on his own and living life on his terms. Even though he often questioned his own morals, he made good decisions, and generally did the right thing.