After completing his assignment to construct the Pentagon, a reluctant Lieutenant General Leslie R. Groves is ordered to supervise “The Manhattan Project" and beat the Nazi’s in building the first atomic bomb. He first believes the project is a “boondoggle” until he meets Leo Szilard in Chicago, Illinois. The famed scientist explains to Groves that the creation of an atomic bomb is indeed possible. In October 1942, Dr. J. Robert Oppenheimer is called to a northern California airport to meet with Groves and asked to lead the scientific team. When Oppenheimer states that his politics may get in the way, Groves confesses that “higher ups” are worried by it, but he has decided Oppenheimer’s brilliance justifies the risk. However, he warns Oppenheimer that his intellect does not outrank Grove’s brigadier general’s star. Oppenheimer’s wife Kitty persuades him to accept the job. In April 1943, Groves arrives at Los Alamos, New Mexico, to find the camp unfinished. After bawling out a Colonel, and demanding more men, he lectures scientists on the importance of secrecy. Groves silences the murmurs of protest by declaring the only word he will not tolerate is “impossible.” Later, Michael Merriman reports late to camp explaining that he was told the facility did not exist. He meets his roommate, Capt. Richard Schoenfield, MD, the camp physician. They attempt to move a refrigerator up the stairs, but the appliance slips from their hands and smashes through a banister to the floor below. Merriman attends a meeting, in which Oppenheimer explains the scientists have nineteen months to create a bomb based only on a theory. The initial design, which called for the bomb to be fired from a cannon, is rejected, and Oppenheimer creates “free think” teams. Merriman is paired with William "Deke" Parsons, who accidentally squeezes an orange and realizes that if they built a sphere, they could use explosives fired inwardly to compress the radioactive fuel, thus causing fusion. They barge into Oppenheimer’s quarters and drag him to the canteen to discuss their theories with the other scientists. Groves explodes when upon learning of the scientists’ public debate and orders Oppenheimer to compartmentalize his teams so they do not know what the others are doing. Oppenheimer counters that access to information is a core principal of science. The scientists rebel against the military restrictions and call a meeting to protest. Groves makes a deal that Oppenheimer will handle all security in the laboratories. However, all discussions of the project must remain behind closed doors. That night, Kitty Oppenheimer throws a party for Groves to suggest they become allies, but the general rejects her, declaring that a wife’s duty is to support her husband. At the party, Merriman is introduced to Schoenfield’s nurse, Kathleen Robinson. Later, Groves learns that Oppenheimer has telephoned his mistress, Jean Tatlock, a known communist. When a Federal Bureau of Investigation (FBI) agent suggests Oppenheimer be removed from the project, Grove growls that Oppenheimer is the project. A few days later, a bomb misfires at the test sight, wounding a solider. Merriman rushes through a field of exploding charges to drag the man to safety. He is ordered to the hospital for tests where he exchanges life stories with Kathleen Robinson. Meanwhile, Grove confronts Oppenheimer about Jean Tatlock and orders the scientist to end the relationship. In January 1944, Oppenheimer travels to San Francisco, California, to breakup with Jean. Although he tells her they are through, she begs him to spend the night with her. The next morning, Oppenheimer tells Jean his work is more important than their relationship and leaves. Months pass and Groves wages a bureaucratic war to keep Los Alamos and his scientists supplied. A two-star general warns him that when the war is over he will have to pay for his “high handed” behavior. In April 1944, Groves receives intelligence that Germany has abandoned attempts to make an atomic bomb. Fearing that the “Jewish element” of his scientists will lose interest in the bomb once Hitler is gone, Groves suppresses the information. Meanwhile, Oppenheimer is testing another compression bomb when he receives a letter stating that Jean committed suicide. As he sits stupefied, the test is a success, opening the way to an implosion device. Oppenheimer tells Groves he cannot work on the bomb any longer, but the general declares that if any other country develops the bomb before the United States, it will be Oppenheimer’s responsibility. In May 1945, while Merriman and Oppenheimer examine equipment to test a chain reaction using Uranium, a loud speaker announces that Germany has surrendered. As the camp explodes into celebration, Oppenheimer tells Groves that Japanese technology is incapable of building an atomic bomb and the reason the A-bomb is no longer valid. However, Groves convinces Oppenheimer that he will be hailed as a hero for giving his country the ultimate weapon. That night, Kitty Oppenheimer asks her husband if he is thinking of resigning. Oppenheimer explains that if he quit he would be come unemployable, and atomic power could be a new energy source for mankind. As the bomb test date nears, the scientists begin having doubts about the morality of actually using it. Merriman, who is going home to visit his family in Chicago, is asked to bring back a petition that scientists at the University of Chicago are circulating to protest deploying the bomb. In July, Oppenhiemer visits Groves in Washington, D.C., and voices the scientists’ concerns, but the general dismisses their “crisis of conscious,” demanding to know how Oppenheimer will explain to a Senate committee that they spent $2 billion for nothing. That night, Groves meets the Secretary of War, Henry Stimson, who informs him that the scientists have been attempting to reach the President to talk him out of using the bomb. Groves instructs military intelligence to pressure Oppenheimer about his communist connections. Grove tells Oppenheimer he is trying to protect him, but the petition is making it impossible. Oppenheimer explains that his men want to demonstrate the weapon publicly to intimidate the Japanese into surrender, but Groves counters that only way to win against Japan is to hurt them so badly they must surrender. They attend a meeting of military and civilian leaders to advise Stimson about using the bomb. An admiral declares the bomb immoral and threatens to resign his commission if it is used. Stimson asks Oppenheimer about a demonstration for a Japanese observer, but Oppenheimer states that if the test failed it would convince the Japanese to hold out, and there would not be enough material for a second test. Back at camp, nurse Kathleen Robinson observes that Merriman is bothered by his work, and she suggests he speak with Oppenheimer. Merriman shows Oppenheimer a copy of the Chicago petition. Oppenheimer insists that scientists are not responsible for how their discoveries are used and instructs Merriman back to work. While he works, Merriman is distracted when a technician drops a cup of coffee. A plutonium sphere rolls out of its protective covering and Merriman is irradiated when he picks it up. Oppenheimer telephones Groves to delay testing the bomb. However, knowing President Truman is meeting with Soviet Union leader Joseph Stalin to negotiate the U.S.S.R.’s joining the war against the Japanese, Groves orders Oppenheimer to stick to the schedule. As Merriman’s health deteriorates, Oppenheimer tries to visit him, but is turned away by security. Dr. Schoenfield confronts Oppenheimer with the knowledge that the government is injecting mentally disabled patients with radiation to see how it affects them. He accuses Oppenheimer of keeping the bomb secret because the American people would reject it if they knew its devastating force. Oppenheimer argues that the bomb is so horrible that it will frighten humanity into a perpetual peace, but Schoenfield counters that he has seen factories being set up to construct hundreds more. At the test sight, scientists tell Groves that prevailing winds could drop radioactive fallout on El Paso, Texas, but the General insists they proceed. The storm passes and preparations for the test resume. Kathleen Robinson sneaks into Merriman’s room and finds him swollen with open sores. She tells him she loves him before Schoenfield makes her leave. Merriman dies. After the bomb is successfully tested, Oppenheimer is paraded before a cheering camp while Kathleen packs Merriman’s belongings.