The Simpsons head for the Springfield Natural History Museum. Bart and Homer discover to their horror that the exhibit is called “Looms, Labor and Liberation—A History of Women Weaving.” Moments later workmen unfurl a banner that reads “The History of Weapons.” To Lisa and Marge’s great disappointment, a museum worker explains that the old exhibit has closed. Homer and Bart are ecstatic. The family heads into the museum, where Homer — along with most of Springfield — cuts in line in front of Ned Flanders. As they make their way through the weapons exhibit, Maggie picks up a switchblade and jabs it towards Marge, who searches her purse for some candy. Lisa attempts to disarm a mock nuclear bomb, while Homer and Bart watch an IMAX 3-D film on nunchucks. Later Homer encounters a talking guillotine, while Bart stretches Milhouse on a rack. As the family heads for the exit, Homer hands his wand-style audio tour (narrated by actress Melanie Griffith) to Flanders, who is still waiting in line to get in. When they’re informed that the weapons exhibit has closed for the day, Flanders and his boys head for an exhibit on evolution. Flanders is horrified by what he sees. He thinks the museum should also include an exhibit on stories from the Bible. He takes his case to the church council, where Lovejoy holds up the Bible and encourages Flanders to take it with a grain of salt. Helen Lovejoy believes the evolution issue can be exploited to “mobilize the flock.” Flanders approaches Quimby on a golf course, and demands that he sign a law that guarantees creationism a place in museums and public schools. Quimby signs the law. Later Principal Skinner announces that the school will present an alternative theory to the origin of man. Lisa is horrified.

Skinner and Miss Hoover present Lisa’s class with an educational film comparing evolution and creationism. The film embraces creationism, and mocks evolution. When Lisa protests, Willie (at Skinner’s urging) pulls a canvas bag over her head. Lisa returns home, and tells Marge about the changes at school. Marge believes it makes sense to give both sides a fair chance, but Lisa insists that creationism and evolution are incompatible. Lisa takes her case to the people during the next town meeting. She again insists that the theories of creationism and evolution cannot co-exist. The idea backfires, and when she returns to school, Miss Hoover announces that the school is teaching only one theory: creationism. Willie grabs away Lisa’s evolution book. The next day, inside a school meeting-room, Lisa addresses a group of nerds. She reads aloud from The Origin of Species by Charles Darwin. Suddenly Wiggum and his men burst through the door, and place Lisa under arrest for teaching non-Biblical science.

In court Lisa is represented by an ACLU-appointed defense attorney, Clarisse Drummond. Prosecuting the case is a country lawyer, Wallace Brady. Drummond calls Professor Frink to the witness stand, but his testimony does not go over well with jurors. Brady calls a scientist who holds a degree in “truthology” from Christian Tech to the stand. This “scientist” maintains that evolution is “hogwash” because of the missing link. Judge Snyder is impressed. He announces that unless Lisa finds the missing link by the next morning, the trial will end. Later Marge picks Lisa’s copy of The Origin of Species out of the trash. After she finishes the book, Marge says that Darwin’s argument is incredibly persuasive. She tells Lisa she might have a way to help her during the trial. When the trial resumes, Drummond calls Ned Flanders to the stand. Flanders insists that man and ape are not related. Then Marge pulls a bottle of beer out of her purse, and shows it to Homer. Homer tries to open the bottle, only to discover it’s not a twist-off top. He begins grunting and snarling like an ape as he tries to get the bottle open. After tiring of Homer’s outbursts, Flanders calls Homer a “monkey-faced gorilla.” Flanders realizes Lisa is right. The judge rules in Lisa’s favor, and Marge thanks Lisa for opening her eyes. Lisa tells Flanders she respects his beliefs, but doesn’t believe religion should be taught in schools… just as scientists shouldn’t be allowed to teach in church.