A 1959 Senate committee questions ex-AEC Chairman, Lewis Strauss, over his actions during Robert Oppenheimer's security hearing, when a revoked Q-clearance ended Oppenheimer's government advisory role. Strauss, who is nominated for Commerce Secretary, alleges the FBI was suspicious of Oppenheimer since his teaching days, well before anti-Communist William Borden accused him of espionage in 1954. He claims to not have acted against Oppenheimer, despite having many public disagreements with him. In the 1930s, Oppenheimer teaches at Caltech and Berkeley, after studying theoretical physics in Europe. Many Berkeley academics are also Communist Party members, but Oppenheimer does not join himself. After World War II breaks out, Ernst Lawrence of the Radiation Lab, cautions Oppenheimer against having communist connections. Oppenheimer scales back, and is approached by General Leslie Groves to lead the Manhattan Project. Oppenheimer proposes a new laboratory at Los Alamos, New Mexico, where they could endeavor to build an atomic bomb before the Nazis. Edward Teller is recruited to Los Alamos, and theorizes that an explosion would cause (global) atmospheric ignition. While his theory is disproved, he starts researching fusion-based weapons instead of working on the proposed fission bombs. After the War, Soviets test a plutonium bomb, similar to one developed at Los Alamos. In a meeting of top advisors, Oppenheimer frustrates Strauss by favoring arms talks with Russia instead of escalating with Teller's proposed thermonuclear weapons. During a heated period of discussion, Oppenheimer's past security lapses are brought up, including rekindling an affair with Communist ex-lover, Jean Tatlock, immediately after gaining his security clearance in 1942. Oppenheimer also protected his friend Haakon Chevalier from an espionage investigation, by directly lying to security officer, Boris Pash. In his later hearing by the Gray Board at the AEC, the board's counsel, Roger Robb, replays these accusations to make Oppenheimer seem guilty of disloyalty towards the US. In the present, Strauss alleges that Oppenheimer turned scientists against him, starting with Albert Einstein at Princeton in 1947. Teller testifies in Strauss' favor, and David Hill of the Chicago Met Lab is expected to do so too. In July 1945, the Trinity plutonium test is successful, and two bombs are subsequently dropped on Japan. Oppenheimer is labeled 'father of the atomic bomb', but his public stance in the post-war years changes towards nuclear non-proliferation. Irritated at constantly being undermined by Oppenheimer, AEC Chairman Strauss conspires with Borden to initiate the 1954 Gray Board hearing. He appoints Robb as the board's counsel, compromising its independence from the AEC. Oppenheimer's humiliation triggers scientists, who had attested to his loyalty and discretion. At Strauss' Senate hearing, Hill claims the scientific community is against him. Strauss loses the Commerce Secretary nomination and with it, his career. A flashback shows Oppenheimer did not mention Strauss to Einstein at all. Consumed by guilt over bringing atomic weapons to the world, he admits to Einstein that the global catastrophe they feared, and then believed was averted, was now ironically inevitable.

The film begins with Muhammad sending an invitation to accept Islam to the surrounding rulers: Heraclius, the Byzantine Emperor; Muqawqis, the Patriarch of Alexandria; Kisra, the Sasanian Emperor. Earlier, Muhammad is visited by the angel Gabriel, which shocks him deeply. The angel asks him to start and spread the Quran. Gradually, a small number of people in the city of Mecca begin to convert. Observing this, more enemies come and hunt Muhammad and his companions from Mecca and confiscate their possessions. Some of these followers fled to Abyssinia to seek refuge with the protection given by the king there. They head north, where they receive a warm welcome in the city of Medina and build the first Islamic mosque (Quba Mosque). They are told that their possessions are being sold in Mecca on the market. Muhammad chooses peace for a moment, but still gets permission to attack. They are attacked but win the Battle of Badr. The Meccans, desiring revenge, fight back with three thousand men in the Battle of Uhud, killing Hamza. The Muslims run after the Meccans and leave the camp unprotected. Because of this, they are surprised by riders from behind, so they lose the battle. The Meccans and the Muslims close a ten-year truce. A few years later, Khalid ibn Walid, a Meccan general who has killed many Muslims, converts to Islam. Meanwhile, Muslim camps in the desert are attacked in the night. The Muslims believe that the Meccans are responsible. Abu Sufyan comes to Medina fearing retribution and claiming that it was not the Meccans, but robbers who had broken the truce. None of the Muslims give him an audience, claiming he "observes no treaty and keeps no pledge". The Muslims respond with an attack on Mecca with many troops and "men from every tribe". Abu Sufyan seeks an audience with Muhammad on the eve of the attack. The Meccans become very scared but are reassured that people in their houses, by the Kaaba, or in Abu Sufyan's house will be safe. They surrender and Mecca falls into the hands of the Muslims without bloodshed. The pagan images of the gods in the Kaaba are destroyed, and the very first azan in Mecca is called on the Kaaba by Bilal ibn Rabah. The Farewell Sermon is also delivered. The film ends with the narrator discussing the legacy of Islam, followed by actual footage of worshipers making tawaf around the Kaaba in recent times. The end credits feature a montage of footage from various mosques around the world as the adhan echoes throughout them all and Muslims gather to pray in congregation.

In the 1920s, in the town of Hillsboro, Tennessee, a female voice sings " Old-time Religion " as schoolteacher Bertram Cates is arrested for violating state law by conducting a lesson on Charles Darwin 's Descent of Man. The event makes headlines around the world. Matthew Brady, statesman, three-time presidential candidate, and Biblical scholar, volunteers to assist Prosecutor Tom Davenport. A huge parade welcomes Brady, who asks Rev. Jeremiah Brown to stand beside him as he addresses the crowd. Witty and cynical E.K. Hornbeck of the Baltimore Herald, an influential newspaperman, seizes the opportunity to announce that Cates's defense attorney, provided by the newspaper, will be the equally well-known Henry Drummond, one of America's most controversial legal minds and a notorious agnostic. Tourists flood the town. Welcoming Drummond, Hornbeck takes him on a tour of the circus Hillsboro has become. Meanwhile, in the courtroom, Judge Coffey deals with reporters, photographers, and local political interests. Later at the hotel, Brady, his wife Sarah, and Drummond reminisce, regretting the loss of the close friendship they once had. That night, Rev. Brown rallies the townspeople, calling down God's vengeance. When his daughter Rachel, who is engaged to Cates, protests, he condemns her. Admonishing Brown’s harshness, Brady quotes Proverbs 11:29: "He that troubleth his own house shall inherit the wind," sending the crowd home. Breaching Rachel’s confidence to him and Sarah, Brady calls Rachel to the stand, compelling her to tell how Cates left the church when her father declared that a child who drowned was not worthy of heaven because he was not baptized. Overzealously, Brady browbeats a distressed Rachel; Cates instructs Drummond not to cross-examine her, even though her testimony of Cates’s doubts has damaged him with the jury. Drummond intends six scientists as witnesses, but the prosecution successfully objects. Frustrated, Drummond gives an impassioned speech of the consequences of allowing an outdated law to prevail, turning progress backward. He asks to withdraw from the case. The judge orders him to show cause the next morning why he should not be held in contempt. John Stebbins, the father of the drowned boy, offers his farm as collateral for Drummond's bail. That night, the crowds march with a burning effigy chanting that Cates should be hanged. When Drummond tells Hornbeck he needs a miracle, Hornbeck tosses him a Bible, scornfully exclaiming, "Here's a bagful!" Drummond clasps the Bible to his chest, smiling. In court, Drummond makes the unprecedented move of calling Brady—the opposing counsel —as an expert on the Bible, since he has been barred from presenting scientific experts. Brady welcomes this challenge, but he becomes increasingly flustered by Drummond's questions on Biblical inconsistencies and absurdities, such as the “seven days” of creation and Jonah surviving being swallowed by a whale. Brady admits to being unfamiliar with Darwin’s On the Origin of Species. Exposed for his lack of intellectual curiosity, a humiliated Brady is forced to admit that Biblical passages cannot be interpreted literally. He falls into Drummond’s trap to cast doubt on the Bible as the sole credible explanation for human existence. WGN Radio is in court to announce the guilty verdict. Bowing to political pressure not to give a harsh punishment that would aggravate global opinion of Hillsboro backwardness, the judge fines Cates only $100, which Drummond says he will appeal. A disappointed Brady tries to enter a speech into the record, but Drummond successfully moves that the court be adjourned and the crowd begins to leave. As Brady attempts his speech, which few remain to hear, he collapses and dies. Alone in the courtroom, planning the obituary, Hornbeck asks Drummond what Brady said to Rev. Brown, to which Drummond cites Proverbs 11:29 chapter and verse. Hornbeck marvels at how Drummond can quote scripture yet call himself an agnostic. Drummond accuses Hornbeck of being a heartless cynic, a lonely man who will be buried alone. As he leaves, Hornbeck responds confidently that Drummond will be there. Drummond picks up the Bible and Darwin's book in either hand, balancing them as the voice from the beginning sings, " Mine eyes have seen the glory …". Drummond slams the books together, and he walks out with them under his arm.