In writing and directing Oppenheimer, Christopher Nolan wanted to present an unbiased view of a misunderstood and often reviled man, J. Robert Oppenheimer (played by Cillian Murphy).
The film is not told in traditional way. Instead, it is set in three different, but connected, time periods and frequently jumps between them. The first time period is post-war life (mainly focused on his security clearance being questioned), his time during the Manhattan Project, and his early life during college.
The film begins in Oppenheimer's post-war life, during which time he became enemies with Admiral Lewis Strauss (played by Robert Downey Jr.). Throughout his life, Oppenheimer dabbled in left wing politics but never became a member of the Communist party. Still, Strauss used this fact, as well as Oppenheimer's wife's membership in the Party, to instigate a review of Oppenheimer's security clearance as a way to get back at him because of a personal grudge. This section of the film is told in black and white, underscoring Strauss' simplicity and the unjustness of the hearing. The security clearance hearing is happening for one reason and one reason alone: Strauss' petty grudge. Despite Oppenheimer's contribution to the safety and security of the United States, he was public ally lambasted for his political beliefs. The dichotomy between the American flag and it being the land of the free and the hearing, which punished Oppenheimer for making a free choice, underscores the stifling political environment of the 1940s and 1950s as much of the country grappled with Communism's effects on their lives.
Next, the film follows Oppenheimer during his time in college as he navigates the relational difficulties that so often come with difficult programs. He clashes with his tutor, who he grows to resent and ultimately tries to kill with a poisoned apple. But he also learns of the power of the atom, Adolf Hitler and his Nazi party (because he finishes his graduate degree in Nazi Germany after starting it in England), and the ingenuity of German scientists, particularly Werner Heisenberg. He takes that knowledge with him to begin a teaching career and later, start the Manhattan Project.
At the same time, Oppenheimer contends with a messy personal life. He has an affair with his soon-to-be-wife, Kitty, and gets her pregnant. Later, he has an affair with several other women, most notably Jean Tatlock. Before introducing viewers to his extramarital affairs, viewers had a relatively rosy picture of Oppenheimer. Yes, he is a flawed man. But viewers haven't seen him do anything morally wrong. The inclusion of his affairs does two things. First, it gives complexity to his character and shows viewers that, despite his good qualities and accomplishments, he is still a mortal man. Second, it creates conflict in the film by showing his moral duplicities. He is willing to engage in immoral or otherwise questionable activity to serve his own needs, just like his involvement in the Manhattan Project and his later mea culpa about his work on the project, which the next part of the film shows.