In 2004 the school board in Dover, Pennsylvania orders science teachers to read a statement calling intelligent design an alternative to evolution, and eleven parents sue, setting up a six-week federal trial before Judge John E. Jones III. NOVA reconstructs the case with courtroom reenactments built from trial transcripts, alongside interviews with the parents, the school board members who pushed the policy, and the scientists and lawyers who argued it out. Biologist Kenneth Miller and other expert witnesses walk through the biochemistry intelligent design proponents cite as evidence of design, including the bacterial flagellum, and explain why the scientific community rejects it. The film also traces intelligent design's paper trail back through earlier creationist textbooks, evidence that became central to the plaintiffs' argument that the concept is religious rather than scientific. Jones, a Republican appointee, ultimately rules that intelligent design is not science and bars it from Dover classrooms, a decision the film presents in his own words, and one that reads as much sharper than anyone expected going in.