While Lisa and her classmates conduct an archaeological survey, a skeleton with abnormal bone structures growing from the shoulders is uncovered, leading the townspeople to conclude the remains are that of an angel.
As Homer attempts to get a motorboat, a new shopping mall in Springfield is being built on an area where a large number of fossils were found. Lisa condemns and protests the building of the mall. Thanks to her protest, it prompts the school to conduct an archaeological dig. When Lisa is digging, it reveals 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; however, Lisa is skeptical, believing it may not actually be an angel, and even has Stephen Jay Gould test a sample of the skeleton. The next day, Dr. Gould runs to the Simpson house and said the tests came out inconclusive and after Lisa on television compares belief in angels to belief in unicorns and leprechauns, Springfield's religious zealots riot and destroy all of the scientific institutions. In keeping with the typical collective Springfield intelligence, the victims of this rampage include a Christian Science library. Lisa goes into the garage to destroy the skeleton; however, it has disappeared. A mob soon converges on The Simpson household, and Lisa is promptly arrested and put on trial for stealing the skeleton. However, before the trial can proceed, the courtroom's attention is diverted when Lenny announces that the skeleton is outside.
When the skeleton reappears, it carries a foreboding message that The End will come at sundown. As for science vs. religion, Judge Snyder issues a restraining order that keeps science and religion 500 yards apart at all times. Sundown approaches, and Springfield's citizens are frightened, but nothing catastrophic occurs. Lisa gets prepared to tell off everyone and when she begins, the skeleton suddenly yells "Prepare for the end... the end of high prices!" and is hoisted over to the entrance of a new discount shopping mall. Lisa realizes that the "end is near" saga was actually a publicity stunt for the mall as a way to exploit the deepest beliefs of people, and calls for a boycott of the mall. However, the bargain-hunting public still go shopping immediately. Dr. Gould also confesses to Lisa that he actually did not do any testing. In the end Marge points out to Lisa that, despite all her skepticism, for a few seconds while it was rising Lisa truly believed the Angel was real. Lisa denies this, but thanks her mother for her support in her moment of weakness.