After visiting an evolution exhibit, Ned Flanders pushes Mayor Quimby to appoint Reverend Lovejoy as a "Morality Czar" in charge of spreading the theory of creationism. Darwin's theories are quickly outlawed and Lisa finds herself as the only supporter of the scientific theory. Lisa is later arrested for holding secret evolution classes and is forced to defend her beliefs in front of a judge. In the 11th hour, Marge stumbles across one of Lisa's textbooks, changes her view and helps her daughter to call Ned Flanders to the stand. Homer's antics cause Ned to crack under pressure and call Homer an ape which leads the judge to believe that Homer resembles the missing link that the prosecutors were basing their argument and the case falls apart.