Hornbeck, the always cynical newspaper columnist, arrives in Hillsboro and instantly begins to extol his wisdom about the issue of Evolution versus Creationism. Hillsboro is in a state of excitement over Brady's arrival. When he does arrive, he is fawned over by the townsfolk, made an honorary Col. in the state militia, and fed a hearty dinner, despite the objections of his wife, Sarah.
After Brady and the rest of the town have headed off, Hornbeck is left to talk to Bert's girlfriend, Rachel Brown. She is the Rev. Brown's daughter and is torn between her beliefs and her love for Bert. Hornbeck attempts to explain how Bert's actions were justified and that Brady's arrival should not be construed as a sole reason for his guilt. They part company. Drummond, preceded by his own shadow from a fiery sunset, meets Hornbeck and is led off.
We join the jury selection phase of the trial a few days later. Brady and Tom Davenport, the DA, exchange barbs with Drummond over several potential jurors with the Judge serving more as a ring master than a voice of the law. Once the court adjourns, Rachel and Bert are left with Drummond. Rachel pleas with Bert to stop fighting. Bert begins to falter and Drummond doesn't object to Bert's desire to give in, but he does demand that Bert do so only if he really thinks what he did was wrong. Bert chooses to fight, leaving Rachel shaken and Drummond satisfied that he is fighting the good fight.
Later that evening is a bible meeting led by Rev. Brown. With Brady seated on the platform with him, Rev. Brown begins a "Fire and Brimstone: speech against Bert. He becomes so zealous that when Rachel pleas for Bert, Rev. Brown calls for retribution against his own daughter. Brady steps in to prevent the unfortunate incident from progressing too far. The crowd disperses leaving Brady and Drummond to speak. Brady asks him why they have moved so far apart. Drummond replies with his own theory about Brady moving away by simply standing still. He walks off leaving Brady puzzled as the Act 1 ends.
The second act opens in the courtroom with Howard, a student in Bert's class, on the witness stand. Brady uses his charm to carefully lead Howard down the "right" path, ending his examination with a biased speech against evolution. Drummond retorts by showing that Howard has the right to think and hear new ideas. Howard is dismissed and Rachel is next to take the stand. Brady has Rachel explain why Bert stop going to church. In doing so, her loyalty to her father intercedes, forcing Bert burst out and explain the real reason why he stopped going. Brady then carefully maneuvers Rachel into a second trap where she tells the jury about Bert saying "God created man in his own image and Man returned the favor." Rachel, realizing that her every word makes Bert appear more guilty, becomes so flustered that she leaves the witness stand before Drummond has a chance to try and salvage his case. Brady rests his case. Drummond begins his defense by calling three prominent scientists to the stand. Each is refuted by Brady. The Judge upholds Brady's objection and declares the witnesses possible testimony as irrelevant to the case.
Drummond takes a moment to recompose himself from these two enormous blows to his case. He appears to have no solution to the problem when he stumbles upon a possible way out. He calls Brady to the stand as an expert on the Bible. Despite the objections of Tom Davenport, the Judge allows Brady to take the stand. Very carefully, Drummond uses Brady's own testimony to show how God intended man to think and not take things as blind truths. Establishing man's gift of thought, allows Drummond to eventually force Brady to admit that "perhaps the first day was of indeterminate length". Finally, Drummond goes after Brady's expert qualifications getting him to admit that God speaks to him. Drummond seizes the moment and uses this to destroy Brady's credibility. Brady feebly tries to defend himself, but is no match for Drummond's verbal onslaught. Brady is left on the witness stand, simply repeating the names of various prophets, with Sarah consoling him.
The final scene opens with Drummond strolling through the courtroom. Brady is unusually serious and quiet. Bert and Drummond are still concerned about the case. With reporters in place and even a radio man on the scene, the court is called to order by the bailiff, Mr. Meeker, and the verdict is read. Bert is found guilty of breaking the law, but the Judge just sets down a $100 fine. Tom Davenport objects., but Drummond shocks everyone by declaring that despite the leniency of the court, he intends to appeal the verdict to the Supreme Court if necessary. Everyone is in an uproar when Brady tries to speak, but his words fall on deaf ears, even the radio listeners. Brady collapses and is rushed out of the court room. His sudden departure leaves Bert, Rachel, and Drummond to discuss the case. When word of Brady's death reaches them, Hornbeck takes his final digs into Brady before Drummond turns on Hornbeck angrily. Hornbeck exits confused by Drummond's sudden compassion for Brady. Bert and Rachel say their good-bye's to Drummond and leave him alone with a copy of the Bible and the Origin of Species. Drummond takes both and weighs them against each other and slaps them together. As he walks out of the courtroom, the doors close behind him.