While watching a 1950s science fiction movie, Bart and Lisa see a commercial for a model rocket kit and Bart orders it by using Homer's credit card number. Homer helps Bart and Milhouse build it, but it blows up before launching. Jealous that Ned Flanders built a superior rocket, Homer enlists the help of his former nerdy college roommates, Gary, Doug, and Benjamin, to build a rocket piloted by the hamster Nibbles. The rocket lifts off successfully, but it develops complications and Nibbles bails out. However, Homer makes an attempt to shoot down the rocket with a 12 gauge shotgun, but the rocket crashes into the church. The church council meets up to decide how to come up with money to fund the repairs to the church, and with no other aid available they accept help from Mr. Burns and Lindsay Naegle. The two rebuild the church as a commercial monstrosity, complete with advertising signs, a Lard Lad statue, and a Jumbotron. Lisa is appalled at this and abandons the church, feeling her religion has lost its soul.
That night, Lisa prays to God and assures him she has not turned her back on him, but plans to seek a new path to him. While on a walk around town passing many sacrilegious signs, she finds Springfield's Buddhist temple. Inside she sees Lenny and Carl meditating, and Hollywood actor Richard Gere teaches the core concepts of Buddhism to her. An intrigued Lisa takes a pamphlet on Buddhism and studies it at home. It convinces her of the virtues of the faith, and Lisa announces out her window she has become, and forever will be, a Buddhist. Lisa plants her own bodhi tree in the back yard and begins to meditate, but Marge grows increasingly worried about Lisa's soul and tries to convince her to come back to Christianity.
At the church council, Reverend Lovejoy tells Marge to use Christmas to bribe her back. Marge bakes cookies, decorates the home, and has Ralph and Milhouse dress as a pony in wrapping paper to tempt her, but Lisa runs from the home when she realizes what is happening. At the Buddhist temple she tells Richard Gere her family tried to trick her, but Gere informs her that while Buddhism is about one finding inner peace, it is also about respecting the diversity of other religions based on love and compassion - thus, Lisa is free to celebrate any holiday with her family including Christmas. Lisa goes back home, falling asleep beside the Christmas tree and tells everyone that she will be celebrating Christmas with them and continue paying lip service to Christianity while practicing Buddhism for the rest of her life. As Marge takes her to the kitchen to get some cookies for her, Lisa asks about her pony, and Marge tries unsuccessfully to change the subject as Lisa calls out for her gift.