Muff Potter has been accused of the murder of Dr. Robinson. One night, he went along with the doctor and Injun Joe on a grave-robbing expedition at the local cemetery. The men got into an argument, and Injun Joe stabbed Dr. Robinson to death. During the melee, Muff got knocked out, and when he came to, Injun Joe was long gone, leaving him as the only plausible suspect for the doctor's murder.

Fortunately for Muff, Tom and Huck witnessed everything. At first, they're reluctant to come forward and tell the sheriff what happened. They're scared of what Injun Joe might do to them if they spill the beans. But eventually, they realize that Muff's heading for the gallows if they don't confess what they saw that terrible night. So they take the witness stand in the trial of Muff Potter and pin the blame on Injun Joe, who makes a sudden, daring escape, diving through the courthouse window.

Muff Potter is arrested because he is believed to have murdered Doctor Robinson. In reality, it was Injun Joe who killed the doctor. Early on in the novel, Potter, Joe, and Robinson appear to be working together to rob graves in the local cemetery. An argument breaks out, Potter is knocked unconscious, and Joe kills Robinson with a knife. After these events, Potter is framed for murdering Robinson and subsequently arrested. Though many other events take place in the novel, this grisly act of murder functions as the plot's centerpiece and contributes to most of the drama. Luckily, since Tom Sawyer (along with Huck Finn) witnesses the murder in the cemetery, he is able to clear Potter's name before he is unjustly condemned for a murder he didn't commit.