Just before chapter 13 begins, Becky Thatcher finally returns to school. Tom is happy and begins showing off in front of her. Unfortunately, Becky isn't at all pleased with Tom's antics.
She turned, with her nose in the air, and he heard her say: "Mf! some people think they’re mighty smart—always showing off!"
Tom is crestfallen, and his depression deepens. He's been stressed and anxious about his standing with Becky, he's nervous about having witnessed Injun Joe kill a man, and he's unsure of whether or not to tell the town that Injun Joe is lying. He feels terrible, he feels alone, and he feels that there is a general lack of sympathy being directed at him. Because of these feelings, Tom decides to run away and lead a life of crime.
Tom's mind was made up now. He was gloomy and desperate. He was a forsaken, friendless boy, he said; nobody loved him; when they found out what they had driven him to, perhaps they would be sorry . . . Yes, they had forced him to it at last: he would lead a life of crime. There was no choice.
Tom is about to leave when he comes across Joe Harper. Joe is feeling equally unloved because his mother just hit him for drinking some cream. Joe was actually coming to find Tom. Joe planned on asking Tom if he wanted to run away with Joe.
But it transpired that this was a request which Joe had just been going to make of Tom, and had come to hunt him up for that purpose. His mother had whipped him for drinking some cream which he had never tasted and knew nothing about; it was plain that she was tired of him and wished him to go; if she felt that way, there was nothing for him to do but succumb; he hoped she would be happy, and never regret having driven her poor boy out into the unfeeling world to suffer and die.
The two boys then set out to run away, and they decide that becoming pirates is definitely the trade that they want to pursue. They decide that Jackson's Island is the ideal location for their new pirate lives.
Three miles below St. Petersburg, at a point where the Mississippi River was a trifle over a mile wide, there was a long, narrow, wooded island, with a shallow bar at the head of it, and this offered well as a rendezvous. It was not inhabited; it lay far over toward the further shore, abreast a dense and almost wholly unpeopled forest. So Jackson’s Island was chosen.
Before leaving, they decide that they need some supplies. The two boys don't bring much. They bring some "hooks and lines," and Tom brings a "boiled ham and a few trifles." Joe brings some bacon, and Huck (who has now joined the pirate crew) brings a skillet, some tobacco leaves, and a few "corn-cobs to make pipes with."
The boys then shove off on a raft, and head down the river. At first, they are all having a great time being pirates on the run; however, as they are falling asleep on the first night, the boys begin feeling guilty about running away from home and stealing supplies.
Then at once they reached and hovered upon the imminent verge of sleep—but an intruder came, now, that would not "down." It was conscience. They began to feel a vague fear that they had been doing wrong to run away; and next they thought of the stolen meat, and then the real torture came . . . it seemed to them, in the end, that there was no getting around the stubborn fact that taking sweetmeats was only "hooking," while taking bacon and hams and such valuables was plain simple stealing — and there was a command against that in the Bible.
The three boys decide that to appease their conscience, they must become pirates that never steal anything.
So they inwardly resolved that so long as they remained in the business, their piracies should not again be sullied with the crime of stealing. Then conscience granted a truce, and these curiously inconsistent pirates fell peacefully to sleep.
Tom decides to run away "to escape from hard usage and lack of sympathy at home". He has been downhearted because of the murder he witnessed, and because Becky Thatcher has not been at school, and his Aunt, thinking he has been sick, has unsympathetically been making him take some nasty "Painkiller". Then, when Becky returns to school, she first ignores Tom then treats him with disdain. Tom is running away to get back at them.
Joe is running away for similar reasons. His mother has whipped him for something he says he didn't do, and he is angry. Tom and Joe decide to become pirates, and invite Huck Finn along. They will meet on the riverbank two miles above the village, take a raft, and row over to Jackson Island on the Mississippi. Each boy will bring hooks and lines, and whatever he can steal. Tom brings a boiled ham and "a few trifles", Joe brings a side of bacon, and Huck brings a skillet, some leaf tobacco, and corncobs with which to make pipes. As the boys, having settled on the island, fall asleep, Tom and Joe begin to feel guilty about running away, and about stealing the meat and other things (Chapter 13).