When Rev. Lovejoy disciplines Bart for a prank he pulled in church - he tricked the organist into playing Iron Butterfly's ""In-A-Gadda-Da-Vida" - he and co-conspirator Milhouse begin arguing over whether man really has a soul. Bart scoffs at the notion and agrees to "sell" his soul (a piece of paper with the words "Bart Simpson's Soul") to Milhouse for $5. A series of situations makes Bart realize maybe he really did sell his soul, prompting him to go all-out to get it back from Milhouse, who isn't willing to sell. Meanwhile, Moe attempts to open a family-style restaurant inside his tavern, with the gimmick that if he doesn't smile when servicing a customer, the meal is free. Moe's surly demeanor and the stress of running such a business alone conspire to do the establishment in.
- When the Church's opening hymn is replaced with "In-A-Gadda-Da-Vida," Reverend Lovejoy suspects one of the children is to blame. Out of guilt, Milhouse snitches that Bart did it.
Both Bart and Milhouse are put to work cleaning the church's pipe organ, where Bart chastises Milhouse for telling on him. Milhouse claims that he doesn't want his soul pecked at by crows, but Bart claims that there is no such thing as a soul. Hearing Bart speak vehemently about this, Milhouse offers to buy Bart's soul for $5. Bart signs a piece of paper with the words "Bart's Soul," and gives it over to Milhouse.
Bart uses the money to buy some 'growing dinosaur' figures, but soon after, is surprised by a number of things. The automatic door at the Quik-E-Mart doesn't open for him, his breath doesn't show up when he blows on the ice cram cooler there, and he doesn't find the Itchy-and-Scratchy show funny.
Lisa feels that Bart may really have lost his soul, and Bart goes to Milhouse to buy it back. However, Milhouse will only sell it back for $50, which Bart refuses. Later on, Bart has a dream in which he is in a land with the other kids, and each one has a soul to play with. As they take to rowboats, Bart's soul can be seen with Milhouse and his soul. Both souls row Milhouse's boat, but Bart is unable to row his, as he's alone.
Over at Moe's, Moe is dulled by the fact that his bar is not picking up a larger clientele. After a pricey construction job, 'Moe's' becomes 'Uncle Moe's Family Feedbag.'
The Simpsons eventually go there, but upon Lisa delivering a meal blessing mentioning 'souls,' Bart rushes off, intent to get his soul back.
Meanwhile, Moe's short-temper is tested by a number of patrons, before he finally snaps, causing everyone to walk out. Moe then restores the bar to its original format.
Bart eventually gets to Milhouse's house, but finds it being fumigated for potato bugs. The exterminator tells Bart that the family went to Milhouse's Grandmother's place, and Bart runs through the darkened city streets, before finally getting there.
Bart begs Milhouse for his soul back, but Milhouse tells Bart that he traded his soul to the Comic Book Store guy for some ALF pogs.
When Bart goes to buy his soul back, the Comic Book Store Guy claims he already sold it to an unnamed party, except to say they were "most interested in the purchase of a little boy's soul."
Going home, Bart prays that he's afraid, and just wants his soul back. It is then that Lisa gives him back the paper, and claims that she bought it for him. However, she tells Bart that some people believe that one has to earn their soul through turmoil and strife, such as he has gone through.
In the end, Bart eats the piece of paper to regain his soul, and that evening, has another dream, in which he and his soul are rowing a boat with the other kids. However, they both bump into Martin Prince's boat, knocking Martin into the water, as Bart and his Soul laugh.