Reverend Lovejoy punishes Bart and Milhouse for a prank by making them clean the church organ. While performing the tedious chore, Bart claims that people do not possess souls. Milhouse counters that if Bart is so sure about his belief, he will give him five dollars in exchange for his soul. Thinking Milhouse a simpleton, Bart writes “Bart Simpsons’ Soul” on a piece of paper and sells it to his friend. Shortly thereafter, Bart notices strange things happening: Santa’s Little Helper and Snowball II suddenly dislike him, Itchy & Scratchy cartoons no longer make him laugh, and even pranks on Homer leave him unaffected. After witnessing the change, Lisa suspects that her brother really did lose his soul. Meanwhile, Moe announces to his long-time customers that he’s transforming the bar into a family restaurant to attract more customers.

Lisa convinces Bart that without his soul he’s a hollow shell of his former self. But when Bart approaches Milhouse, hoping to regain possession of his soul, his friend demands 50 dollars for the piece of paper. Meanwhile, Moe celebrates the grand opening of his restaurant, “Uncle Moe’s Family Feedbag.” But in an effort to please his new, younger clientele, the former barkeep buries his tough persona in favor of a kinder, gentler Moe.

Bart returns to the Van Houten residence, but learns that Milhouse and his family have temporarily relocated to Gramma Van Houten’s small apartment miles away so exterminators can irradiate a potato bug infestation. Filled with determination, Bart peddles his bike to the address. But when he arrives, he learns the paper representing his soul was traded to the owner of a comic book store in exchange for pogs. Bart is crestfallen to learn the comic book dealer sold his soul to an unknown buyer. Desperate, Bart preys to God for the return of his soul. Lisa then admits it was she who bought the paper. Overjoyed, Bart devours the piece of paper containing his soul. Meanwhile, Moe’s charade takes its toll. His anger erupts in a violent outburst, and customers flee the restaurant. But Moe realizes he still has the loyalty of his old customers and reopens the bar.