Following a Health convention held in Springfield, the children of Springfield (including Bart) are deemed to be overweight. To help them stay in shape, the parents enroll their children in pee-wee football. The coach, Ned Flanders, helps keep the team undefeated, but Homer heckles him relentlessly. Flanders finally snaps and turns the job over to Homer.
Homer initially acts tough towards Bart, but when he is reminded of how his father was hard on him as a child, he decides to be nicer to Bart (and meaner to his father). The next day, he becomes a lousy coach and decides to cut many players from the team, and replaces star quarterback Nelson with Bart, causing an uproar from the team. Bart is unable to play the position well and causes the team's first loss and ruined their undefeated season; Nelson bluntly threatens Bart's life if he loses again. While training at night Bart meets Joe Namath, who promises to help him, but soon after Joe's wife fixes the car, which had broken down due to vapor lock, Joe leaves without helping Bart.
Lisa suggests that Bart pretend he is injured to get out of quarterbacking, which he eagerly does, but Homer claims that without Bart the team must forfeit. Bart tells Homer that he sucks at being quarterback; Nelson concurs. Homer, still not getting it, encourages Bart yet again to keep at it. This causes Bart to become angry and quit the team. Homer, instead of realizing his own fault, gets angry at Bart and cuts him from the team. Homer also cuts Milhouse, much to Milhouse's delight. Homer and Bart have a fallout. Homer calls Bart a quitter. On the next game, Nelson is made quarterback again and the team wins, but Homer has nobody to celebrate with and becomes lonely. Afterwards, Homer finds Bart and persuades him to rejoin the team. He apologies to Bart for blindly encouraging him for something that Bart was not good at. The next day, during the championship game, the score is tied when Chief Wiggum comes to arrest Nelson. Bart decides to pretend he is Nelson, assuming the charges are minor (they are actually burglary and arson). The team finally wins the championship, and unsuccessfully tries to carry Homer off the field. Joe Namath reappears to give his final thoughts on the episode and on vapor lock, the third most common cause of engine stalling.
The credits show Homer cutting all the people who worked on the episode (except for Joe Namath), including the woman who shushes in the Gracie Films logo.