Mr. Largo is helping the Springfield Elementary School band prepare for their big performance at the state fair. After a suggestion by Lisa that they are doing the same old song, they perform a different song which is James Brown's "Living in America". They perform the song, but lose to Ogdenville Elementary School, who perform "Stars and Stripes Forever" using red, white and blue glowsticks to form a flag, which was against the rules as the competition forbids use of visual aids. After the competition, Lisa accuses Ogdenville of cheating, and she later writes a complaint to President Clinton. At the fair, Homer and Bart see a horse named Duncan being forcefully made to dive from a diving board. Chief Wiggum claims that this is a case of extreme animal cruelty and asks whether Duncan's owner has a permit for said crime. After the man flees, Wiggum announces that someone can either adopt Duncan or let him go to a dog food factory. Bart asks Homer to take Duncan home,but Marge ponders about the idea and Comic Book Guy points out, that in the episode "Lisa's Pony," the family already had a horse, which forced Homer to work extremely long night shifts at the Kwik-E-Mart. Regardless of what he says, the Simpsons take Duncan home and, just as they did in the past, struggle to pay for his needs. It costs them $500 a week to keep him, but Homer and Bart think of a way for Duncan to make money to help offset the costs of keeping him.
Duncan makes an excellent placekicker, but NFL league rules forbid horses from competing. After Homer denounces the rules, Bart discovers that Duncan is a fast runner and suggests that he should be trained to be a racehorse. Homer enters Duncan at Springfield Downs, with Bart (in pajamas) as the jockey. They lose as Duncan refuses to leave the stall until the last minute. Homer and Bart find a new strategy for Duncan to win, by making him into a Dennis Rodman look-alike, renaming him "Furious D," complete with a leather jacket, a new multi-colored mane and Lisa's bracelet as a nose ring. He intimidates the other horses by headbutting several of them, and he and Bart win the race.
They go on to win a series of races until Homer discovers the secret lair of the losing jockeys. They reveal themselves to be magical elf-like creatures, whose depression after losing so many races threatens their normally happy lifestyle. They want him to forfeit the upcoming championship race, threatening to eat his brain if he does not comply. Homer initially considers the idea, though he later cannot bear to tell his son to lose the race, so they decide to win the race anyway and ultimately do so. The furious jockeys chase after Bart and Homer and threaten to kill them, but Homer was prepared for such an event; he calls out to Marge and Lisa who foil the jockeys by spraying them with water and tying them up in a bin bag, presumably, taken away to the garbage dump. As Bart and Homer prepare for Duncan's retirement from racing to live life as a stud (much to Duncan's excitement), President Clinton comes to see Lisa at home and presents her with a plaque, saying that Ogdenville was wrong to use glowsticks and that Springfield Elementary's band is the true champion. He also gives Lisa a moral lesson: "If things don't go your way, just keep complaining until your dreams come true." Marge complains that this is a lousy lesson, to which the President replies "hey, I'm a pretty lousy President."
Some Simpsons fans have an extremely low opinion of "Saddlesore Galactica." The episode contains numerous meta-humor and self-referential jokes centered on how outlandish the show's plots and characters have become, how the newer stories borrow heavily from the older stories, and how the Simpsons fans (particularly those on alt.tv.simpsons) complain of these flaws. Examples of this include the blatant recycling of themes and ideas from earlier episodes (which is pointed out repeatedly by Comic Book Guy, who incidentally is also wearing a "worst episode ever" t-shirt), the plot twists (such as the jockeys being magical elf creatures), and the over-the-top caricaturing of the main characters (such as Lisa being overly activistic after losing the band competition). This has led some to believe that the episode was made outlandish and derivative on purpose, which many fans considered to be an insult towards them (particularly true when the Comic Book Guy pointed out that the Simpsons adopting a horse for a pet was done before, and Homer asking the crowd of people at the fair if anyone cared what The Comic Book Guy thought, to which the crowd yells, "No!").