Marge disapproves of Bart and Milhouse watching South Park, so she unsuccessfully tries to get them to watch Good Heavens on PAX. The boys soon find themselves outside the house and bored, and decide to tie a thread to a fly. When the fly enters the Flanders house and is eaten by a cat, Bart and Milhouse find themselves inside the home, unsupervised. They take the opportunity to cause mischief, and discover Ned's collection of Beatles memorabilia in the basement. They drink from cans of a 40-year-old novelty beverage and start to hallucinate, with Bart seeing Milhouse as John Lennon through various stages of his life. When Ned, Rod and Todd return home and discover the damage caused by Bart and Milhouse, they flee to their panic room and call the police. Chief Wiggum and his crew subsequently catch the boys in the basement, and call their parents and says they will take "The Last Train to Clarksville," then Lou corrects Wiggum and says "That's The Monkees Chief." They decide that Bart and Milhouse should spend all their time under parental supervision. Bart is also forbidden from playing with Milhouse, whom Marge believes incites Bart into his bad behavior.
Marge subsequently establishes a peer group based on Native American life, called the "Pre-Teen Braves." It is composed of Bart, Ralph Wiggum, Nelson Muntz, and Database. Homer takes on the role of tribe leader, but when he fails in his leadership skills, Marge takes over. Later, when Marge takes the boys on a nature walk, they meet a Mohican man who shows them a field that is in need of cleaning up. The "Pre-Teen Braves" agree to the job, but as they are about to begin, they discover that another peer group, the "Cavalry Kids" - led by Milhouse's father, Kirk Van Houten, composed of Milhouse, Martin Prince, Jimbo Jones, and a nerd - have already done it. The two groups decide to go to war, trying to outdo each other in doing good (for example, when the Cavalry Kids used a bulldozer to destroy the house of the homeless from the Pre-Teen Braves and posted a pre-fabricated in place, the Pre-Teen Braves retaliated by setting it on fire with arrows). When they sell candy in the hope of becoming batboys at a Springfield Isotopes game, the "Pre-Teen Braves" try to thwart the "Cavalry Kids" by lacing their candy bars with laxatives. Unfortunately for them, the senior citizens, in need of relief from constipation, buy the "Cavalry Kids" a win.
At the Isotopes game, the "Pre-Teen Braves" make another attempt to defeat the "Cavalry Kids". Bart and Homer divert the "Cavalry Kids" away from the stadium with a fake "free VIP parking" sign, and the "Pre-Teen Braves" then disguise themselves as their enemies before singing their own version of The Star-Spangled Banner. The crowd becomes angered by this, and when the real "Cavalry Kids" arrive, a fight breaks out between everyone. Marge, appalled by this, starts crying, and when this is shown on the Jumbotron, the fighting stops and the Sea Captain suggests that everyone should sing a sweet, soothing hymn like Canada's national anthem instead of a "hymn to war" like The Star-Spangled Banner. Everyone present sings O Canada and joins hands to form a maple leaf on the baseball field.
In the end, Bart and Milhouse sum up the whole experience by saying that they have learned that "war is not the answer —except to all of America's problems."