As Inherit the Wind opens, Bert Cates, having been arrested for teaching evolution to his sophomore science class, is in jail. Rachel Brown, his girlfriend and the daughter of Reverend Brown (the spiritual leader of Hillsboro) visits him. Rachel is confused and torn between the opposing beliefs held by Cates (academic freedom) and her father (fundamentalism) and her love for both of them. Desperately wanting to avoid the mounting controversy over his case, she pleads with Cates to admit he was wrong to teach evolution, and she is disappointed that Cates refuses.
Cates is nervous and frightened because he has learned that Matthew Harrison Brady, three-time presidential candidate, fundamentalist, and leader of the crusade against evolution, has volunteered to be the prosecuting attorney. He reveals to the bailiff, Mr. Meeker, that he has sent a letter to the Baltimore Herald asking for an attorney to defend him.
To celebrate Brady's arrival, the townspeople of Hillsboro carry posters, hang banners, provide a picnic lunch "fitt'n fer a king," and parade through the town singing "Gimme that old-time religion." Brady basks in the adoration of his followers and vows to defend the people of Hillsboro against "Evil-ution." E.K. Hornbeck, cynical columnist for the Baltimore Herald, also arrives in Hillsboro. He openly mocks Brady and is contemptuous of the bigotry and ignorance he observes in Hillsboro. He informs Brady's followers that Henry Drummond, an attorney famous for successfully defending underdogs, has been sent by the Baltimore Herald to defend Cates. Drummond arrives in Hillsboro later that evening. Upon his arrival, the only attention he receives is from Melinda, a young girl who screams that he's the devil.
When the trial begins, the courtroom is full. Both Brady and Drummond are self-assured: Brady, because he has the support of the spectators and is confident that his fundamentalist views are right and will, therefore, prevail; Drummond, because he seeks the truth.
After the first day in court, which involves selecting the jury, Reverend Brown holds a prayer meeting, at which he delivers a fire-and-brimstone sermon. Becoming overzealous, he prays that Cates be destroyed. When his daughter, Rachel, tries to stop him, he condemns her as well. Uncomfortable with the tenor of the prayer and afraid that Reverend Brown's actions may hinder the support the townspeople have in him, Brady steps forward and curtails Reverend Brown's sermon by reciting the wisdom of Solomon.
The following day, the trial proceeds and witnesses are called. Cates' students testify, and Rachel, whom Brady tricked into revealing confidential conversations she'd had with Cates, also testifies. The judge excludes Drummond's scientific witnesses claiming that evolution itself is not on trial. Determined to challenge the Butler Law, Drummond shrewdly switches his tactics and calls Brady to testify as an expert on the Bible. Brady arrogantly and ignorantly agrees to take the stand. Drummond's cross-examination of Brady, in which he exposes that Brady doesn't interpret the Bible literally and destroys Brady's credibility by questioning his status as a self-anointed prophet, changes the course of the trial.
The jury finds Cates guilty, and he is fined $100. Brady protests the minimal punishment. Although he won the case, his victory is a hollow one. The real triumph belongs to Drummond and Cates, who win a moral victory for freedom of thought.
Trying to stem the tide of attention and support that has rapidly drifted away from him, Brady insists on giving his closing speech, despite the fact that court had been adjourned and carnival atmosphere has intruded. Only a few of the faithful followers seem prepared to listen; the others who remain listen only grudgingly. Brady begins his speech, but he is unable to hold the crowd's attention. The final insult occurs when the radio announcer interrupts Brady to return the listeners to their regularly scheduled broadcast. Brady collapses, is removed from the courtroom, and soon after dies.
Rachel enters the courtroom, carrying a suitcase. She apologizes to Cates for her lack of understanding and to Drummond for possibly offending him. She reveals that she has read Darwin's On Origin of Species, and, although she doesn't like the premise of evolutionary theory, she now understands how important having the freedom to think is. She chooses to support Cates and leave her father.
Hornbeck continues to mock Brady after learning of his death, and Drummond defends Brady, angrily pointing out that "Brady had the same right as Cates: the right to be wrong!" Then Drummond leaves the courtroom with a Bible and a copy of Darwin's On the Origin of Species.