Um, this is kind of simple. Act I in the plot analysis is conveniently the same as Act I in the play: all of the important players have arrived: Bert, who's on trial; Rachel, who's his crush and also his adversary's daughter; Brady, the prosecutor; Drummond, the defense attorney; you get the idea.
And we know where the line in the sand is. Some people think evolution is an evil, Godless idea, and it definitely shouldn't be taught in schools. That'd corrupt the young kids' minds even worse than Marilyn Manson, you know? Some people (cough cough, Drummond and the journalist Hernbeck, cough cough) think otherwise.
And, whaddyaknow, Act II corresponds to Act II in the play as well. In this act, arguments are made for both sides. Brady attacks Bert's character, trying to prove that he's a heathen and generally sucks as a person. Drummond attacks Brady and makes him look like a hypocrite and all-around dummy.
So, what's said is said. What's done is done. And the jury is set to deliberate. Nobody knows what's going to happen… unless you've read a history book, that is.
Surprise, surprise: Act III = Act III. Bert's found guilty, but not in the way that Brady had hoped. He gets a slap on the wrist along with his guilty verdict—a fine for a hundred dollars—not a jail sentence.
Bert and Drummond also don't back down; Drummond says that Bert won't even pay the stupid one hundred smackaroos, because they're appealing this case to a higher court. Brady drops dead unceremoniously, and Rachel, Bert, and Drummond get out of town. Fin.