Homer attempts to claim a motorboat from a "police raffle" that turns out to be a sting operation. While returning home, the family passes a new mall in Springfield that is being built on an area where a large number of fossils were found. Lisa protests strongly, which prompts the school to conduct an archaeological dig. During the excavations, Lisa finds a human skeleton with wings. Springfield's residents are convinced it is an angel, and Homer cashes in by moving the skeleton into the family's garage. Lisa remains skeptical, and asks Stephen Jay Gould to test a sample. When Dr. Gould appears at the Simpson house the next day to tell Lisa that the tests were inconclusive, Lisa goes on TV to compare the belief in angels to the belief in unicorns and leprechauns (news anchor Brockman states that leprechauns are extinct). In response, Springfield's religious zealots go on a rampage to destroy all scientific institutions (including, ironically, a Christian Science Reading Room). Appalled with the violence, Lisa goes into the garage to destroy the skeleton, but finds that it has disappeared. The mob soon converges on the Simpson household, and Lisa is promptly arrested and put on trial for destroying the skeleton.
Before the trial begins, the courtroom's attention is diverted when the skeleton appears outside, carrying a foreboding message that "The End" will come at sundown. Meanwhile, Judge Snyder issues a restraining order to keep science and religion 500 yards apart at all times. Sundown approaches, and Springfield's citizens are frightened, but nothing catastrophic occurs. As Lisa starts to reprimand them, the skeleton suddenly silences her and yells "Prepare for the end... the end of high prices!" and is hoisted over to the entrance of the new "Heavenly Hills Mall", now completed after the archaeological dig. Lisa realizes that the "end is near" saga was a publicity stunt for the mall, exploiting people's deepest beliefs, and she calls for a boycott of the mall. The bargain-loving public ignores Lisa and goes shopping. When asked why his tests never indicated the skeleton was fake Dr. Gould confesses that he actually never did the tests. Marge says that, for a few seconds while it was rising, Lisa believed the angel was real. Lisa denies this, but admits she was frightened and thanks her mother for her support.