The film was directed by Roland Joffé and written by Joffe and Bruce Robinson.
In September 1942, U.S. Army Corps of Engineers General Leslie Groves (Paul Newman) who oversaw construction of the Pentagon is assigned to head the ultra-secret Manhattan Project, to beat the Germans in building an atomic bomb.
Groves picks University of California, Berkeley physicist J. Robert Oppenheimer (Dwight Schultz) to head the team of the project. Oppenheimer was familiar with northern New Mexico from his boyhood days when his family owned a cabin in the area. For the new research facility, he selects a remote location on top of a mesa adjacent to a valley called Los Alamos Canyon, northwest of Santa Fe.
The different personalities of the military man Groves and the scientist Oppenheimer often clash in keeping the project on track. Oppenheimer in turn clashes with the other scientists, who debate whether their personal consciences should enter into the project or whether they should remain purely researchers, with personal feelings set aside.
Nurse Kathleen Robinson (Laura Dern) and the young physicist Michael Merriman (John Cusack) question what they are doing. Working with little protection from radiation during an experiment, Michael drops a radioactive component during an experiment dubbed Tickling the Dragon's Tail and retrieves it by hand in order to avoid disaster, but is exposed to a lethal dose of radiation. In the base hospital nurse Kathleen can only watch as he develops massive swelling and deformation before dying a miserable death days later.
While the technical problems are being solved, military investigations are undertaken in order to thwart foreign espionage, especially from 'communist sympathizers' who might be associated with socialist organizations. The snooping reveals that Oppenheimer has had a young mistress, Jean Tatlock (Natasha Richardson), and he is ordered by the military to stop seeing her. After he breaks off their relationship without being able to reveal the secret reasons why, she is unable to cope with the heartache and is later found dead, apparently a suicide.
As the project continues in multiple sites across America, technical problems and delays cause tensions and strife. To avoid a single-point-of-failure plan, two separate bomb designs are implemented: a large, heavy plutonium bomb imploded using shaped charges ("Fat Man"), and an alternate design for a thin, less heavy uranium bomb triggered in a shotgun design ("Little Boy"). The bomb development culminates in a live detonation in south-central New Mexico at the Trinity Site in the Alamogordo Desert (05:29:45 on July 16, 1945), where everyone watches in awe at the spectacle of the first mushroom cloud with roaring winds, miles away.
In the end, both bombs, Fat Man and Little Boy, were successful, ushering in the Atomic Age.
Most of the characters were real people and most of the events real happenings, with some theatrical license used in the film.
The character of Michael Merriman (John Cusack) is a fictional composite of several people and is put into the film to provide a moral compass as the "common man". Part of the character is loosely based on the popular young scientist Louis Slotin. Contrary to Merriman's death in the movie, Slotin's accident and death occurred after the dropping of the two bombs on Japan, and his early death was feared by some as karma after the event; see their respective articles. A very similar mishap happened less than two weeks after the Nagasaki bomb, claiming the life of Harry Daghlian. Both incidents occurred with the same plutonium core, which became known as the Demon core.
Even before Oppenheimer was chosen to be the lead scientist of the Manhattan Project, he was under surveillance by the Federal Bureau of Investigation (FBI), and once selected, the surveillance was intense; every single phone call was recorded and every contact with another person noted. After he was picked to head the laboratory, he only met with Tatlock one time, in mid-June 1943, where she told him that she still loved him and wanted to be with him. After spending that night together, he never saw her again. She committed suicide six months after their meeting.
Filming took place in the fall of 1988 mainly outside Durango, Mexico, where the Los Alamos research facility was re-created. The re-creation of the Los Alamos laboratory entailed 35 buildings and cost over US$2 million to construct in 1988.
The highly dramatic film includes a closely aligned, romantic musical score created by long-time composer Ennio Morricone. Never previously released in any format, the entire score and extra music were released in 2011 by La-La Land Records. The definitive, 2-CD treatment, some of it never before heard, has several cues and portions of others that were dropped from the final cut of the film. Produced by Dan Goldwasser and mastered by Mike Matessino, the CD release includes source cues and alternate takes, as well as exclusive, in-depth liner notes by film music writer Daniel Schweiger. It was limited to an edition of 3,000 copies.
The film has been criticized for distortion of history for dramatic effect, and miscasting in its choices of Paul Newman for the role of General Groves, and Dwight Schultz for the role of Oppenheimer. Noted critic Roger Ebert felt the film lackluster, giving it 1 and a 1/2 stars, and felt that ' The story of the birth of the bomb is one of high drama, but it was largely intellectual drama, as the scientists asked themselves, in conversations and nightmares, what terror they were unleashing on the Earth. "Fat Man and Little Boy" reduces their debates to the childish level of Hollywood stereotyping '. The film holds a 53% rating on review aggregate Rotten Tomatoes
The film made under $4 million on its original release.
The film was entered into the 40th Berlin International Film Festival.