Marge oversleeps, and not having made the children's lunch for the day, Homer makes the lunches instead. Lisa gets a drawing of a sandwich, Bart gets Grandpa's medication, and even these are mixed up. Bart decides to scare an alternative lunch out of his friends by making up a story about a cannibal cafeteria worker named Dark Stanley, who killed all the students in the cafeteria and put them in his kids' head soup after repeatedly being taunted for not graduating from the Massachusetts Institute of Technology. At lunchtime, Bart pretends to be killed by Dark Stanley, leading all of the students to run screaming into the woods while he takes their lunches. Groundskeeper Willie is sent to fetch them all back, but he brings seven extra kids who are Cletus's children. Their names are Whitney, Jitney, Dubya, Incest, Crystal Meth, International Harvester, and Birthday.Principal Skinner tells Superintendent Chalmers that the kids have been refused education in fear that they will lower test averages and cost the school federal funding (after SES has already lost state, county, and local funding), which Lisa overhears. To appease Lisa, Skinner and Chalmers appoint her tutor of the children.
Meanwhile, Skinner punishes Bart by having him spend five sessions with a qualified psychiatrist named Dr. Stacey Swanson (Meg Ryan) (Skinner was going to use the school psychiatrist, but after she freaked out about Dark Stanley, Superintendent Chalmers decided Bart should see someone who was better qualified). Bart is initially unwilling, but Homer insists Bart goes through with it (because there is a Chinese restaurant next door to the psychiatrist where he can get drunk). Initially dismissive, Bart develops a close bond with Dr. Swanson, who uses a Mad Libs-like game and violent video games to get Bart to open up about Homer's alcoholism and other matters. When his sessions end, Bart starts to miss the time he spent with her and enters into a state of depression in which he talks about his problems to an empty chair while lying in bed. He also peeks into her window and sees her counseling Milhouse, and hangs his head while biking in the rain when he looks through a window and sees her dancing with the owner of the Chinese restaurant that Homer had visited earlier in the episode. Marge, worried, uses the funds she had been saving up for Homer's breast reduction surgery to get her son one more session with Dr. Swanson. Bart then reveals that Homer and Marge were young and not ready for parenting when he was born, and that he acts out largely so they will focus on him instead of fighting with each other (the theme of which would be revisited in "Postcards from the Wedge"); he also adds he got the name "Dark Stanley" in part because Homer used to hit him with a Stanley-brand hammer. Bart is happy and leaves therapy feeling good, but Dr. Swanson is visibly saddened when he leaves, and she goes to see her own psychiatrist (Peter Bogdanovich) where she says she cannot stop thinking about Bart. It is revealed during this discussion that "Dark Stanley" was in fact real, and had killed her own son: the therapist believes Swanson is projecting onto Bart, though Swanson claims she is not ready to go into that.
Lisa's initial tutoring efforts are unsuccessful and so she decides to take the children to downtown Springfield to introduce them to culture in the outside world. However, Lisa's plans are diverted when Krusty spots the kids singing, decides to use them as a musical act for his show, and offers them a contract, which Cletus signs with an "X" (in sharp contrast to his elegant signature in the episode "Sweets and Sour Marge"). Lisa is worried about the way that Krusty and Cletus are exploiting the children with their plans for a national bus "No-Collar Comedy Tour", so she sends an e-mail to Brandine, who is currently a soldier in Iraq, and trying to 'stop 9/11' as said by Cletus. She arrives by helicopter to tell Krusty that the contract Cletus signed is null and void, as he is the father of only two of the seven children — the one who cannot sing and the one who cannot ad-lib. The story ends with Cletus telling Brandine that they owe Krusty $12,000, but Brandine tells him that they can live on that, and Cletus is happy to have things back to normal.